{
  "schema_version": 1,
  "phykit_version": "2.4.0",
  "generated_from": [
    "phykit/cli_registry.py",
    "live argparse parsers",
    "docs/_data/command_spec.json"
  ],
  "commands": [
    {
      "canonical": "alignment_entropy",
      "handler": "alignment_entropy",
      "aliases": [
        "aln_entropy",
        "entropy"
      ],
      "entry_points": [
        "pk_alignment_entropy",
        "pk_aln_entropy",
        "pk_entropy"
      ],
      "title": "Alignment entropy",
      "summary": "Shannon entropy across alignment sites",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/alignment_entropy.rst",
      "documentation": {
        "purpose": "Shannon entropy across alignment sites",
        "use_cases": [
          "Shannon entropy across alignment sites"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "alignment_entropy_plot.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/alignment_entropy.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "alignment_length",
      "handler": "alignment_length",
      "aliases": [
        "al",
        "aln_len"
      ],
      "entry_points": [
        "pk_alignment_length",
        "pk_al",
        "pk_aln_len"
      ],
      "title": "Alignment length",
      "summary": "Length of an input alignment",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/alignment_length.rst",
      "documentation": {
        "purpose": "Length of an input alignment",
        "use_cases": [
          "Length of an input alignment"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/alignment_length.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "alignment_length_no_gaps",
      "handler": "alignment_length_no_gaps",
      "aliases": [
        "aln_len_no_gaps",
        "alng"
      ],
      "entry_points": [
        "pk_alignment_length_no_gaps",
        "pk_aln_len_no_gaps",
        "pk_alng"
      ],
      "title": "Alignment length no gaps",
      "summary": "Alignment length excluding gapped sites",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/alignment_length_no_gaps.rst",
      "documentation": {
        "purpose": "Alignment length excluding gapped sites",
        "use_cases": [
          "Alignment length excluding gapped sites"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/alignment_length_no_gaps.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "alignment_outlier_regions",
      "handler": "alignment_outlier_regions",
      "aliases": [
        "aor",
        "outlier_regions"
      ],
      "entry_points": [
        "pk_alignment_outlier_regions",
        "pk_aor",
        "pk_outlier_regions"
      ],
      "title": "Alignment outlier regions",
      "summary": "Detect localized outlier regions in multiple sequence alignments",
      "categories": [
        "Alignment quality & statistics",
        "Homology assessment"
      ],
      "page": "reference/commands/alignment_outlier_regions.rst",
      "documentation": {
        "purpose": "Detect and optionally mask localized sequence regions that are unusually divergent across both alignment columns and individual sequences.",
        "use_cases": [
          "Identify candidate sequencing, assembly, annotation, contamination, or alignment errors",
          "Create a masked alignment without deleting complete taxa or columns",
          "Audit suspicious regions before phylogenetic inference"
        ],
        "input_formats": [
          "Multiple sequence alignments in FASTA, PHYLIP, Clustal, MAF, or Stockholm format"
        ],
        "outputs": [
          "Tab-separated region report on standard output or at --report",
          "Structured JSON report with method, parameters, summary, and regions",
          "Optional FASTA alignment with only flagged characters masked"
        ],
        "errors": [
          "The cutoff must be finite and greater than 1.0",
          "The mask character must be one non-whitespace character other than a gap",
          "Output paths cannot overwrite the input or each other"
        ],
        "limitations": [
          "Calls are statistical outliers and do not prove nonhomology",
          "Very short, very long, or frequently shared errors can be missed",
          "Highly divergent valid regions can be flagged when taxon sampling is sparse",
          "This independent TAPER-inspired implementation can differ from TAPER software output"
        ],
        "scientific_interpretation": "Reported cells are unusual relative to both their alignment columns and the remainder of their sequence. Review important calls and compare analyses with and without masking.",
        "validation": [
          "Synthetic local anomalies are detected while matched control sequences remain unchanged",
          "Identical alignments produce no calls",
          "Unit tests cover scoring, natural breaks, multi-scale smoothing, coordinates, masking, and option validation"
        ],
        "citations": [
          "Zhang C, Zhao Y, Braun EL, and Mirarab S. 2021. TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution. Methods in Ecology and Evolution 12:2145-2158. doi:10.1111/2041-210X.13696"
        ],
        "examples": [
          "phykit alignment_outlier_regions alignment.fa",
          "phykit alignment_outlier_regions alignment.fa --report suspicious_regions.tsv --mask-output alignment.masked.fa",
          "phykit alignment_outlier_regions alignment.fa --mask-character N --json"
        ],
        "related_commands": [
          "alignment_outlier_taxa",
          "spurious_sequence",
          "hidden_paralogy_check",
          "mask_alignment"
        ],
        "related_tutorials": [
          "tutorials/pages/04-evaluating-the-accuracy-of-a-multiple-sequence-alignment.rst"
        ]
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "cutoff",
          "flags": [
            "--cutoff"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "report",
          "flags": [
            "--report"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "mask_output",
          "flags": [
            "--mask-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "mask_character",
          "flags": [
            "--mask-character"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "?",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/alignment_outlier_regions.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--mask-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "alignment_outlier_taxa",
      "handler": "alignment_outlier_taxa",
      "aliases": [
        "aot",
        "outlier_taxa"
      ],
      "entry_points": [
        "pk_alignment_outlier_taxa",
        "pk_aot",
        "pk_outlier_taxa"
      ],
      "title": "Alignment outlier taxa",
      "summary": "Identify outlier taxa in alignments",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/alignment_outlier_taxa.rst",
      "documentation": {
        "purpose": "Identify outlier taxa in alignments",
        "use_cases": [
          "Identify outlier taxa in alignments"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "gap_z",
          "flags": [
            "--gap-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "composition_z",
          "flags": [
            "--composition-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "distance_z",
          "flags": [
            "--distance-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "rcvt_z",
          "flags": [
            "--rcvt-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "occupancy_z",
          "flags": [
            "--occupancy-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "entropy_z",
          "flags": [
            "--entropy-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/alignment_outlier_taxa.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "alignment_recoding",
      "handler": "alignment_recoding",
      "aliases": [
        "aln_recoding",
        "recode"
      ],
      "entry_points": [
        "pk_alignment_recoding",
        "pk_aln_recoding",
        "pk_recode"
      ],
      "title": "Alignment recoding",
      "summary": "Recode alignment into reduced alphabets",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/alignment_recoding.rst",
      "documentation": {
        "purpose": "Recode alignment into reduced alphabets",
        "use_cases": [
          "Recode alignment into reduced alphabets"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "code",
          "flags": [
            "-c",
            "--code"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/alignment_recoding.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "alignment_subsample",
      "handler": "alignment_subsample",
      "aliases": [
        "aln_subsample",
        "subsample"
      ],
      "entry_points": [
        "pk_alignment_subsample",
        "pk_aln_subsample",
        "pk_subsample"
      ],
      "title": "Alignment subsampling",
      "summary": "Randomly subsample genes, partitions, or sites",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/alignment_subsample.rst",
      "documentation": {
        "purpose": "Randomly subsample genes, partitions, or sites",
        "use_cases": [
          "Randomly subsample genes, partitions, or sites"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "mode",
          "flags": [
            "--mode"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": [
            "genes",
            "partitions",
            "sites"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "list",
          "flags": [
            "-l",
            "--list"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "partition",
          "flags": [
            "-p",
            "--partition"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "number",
          "flags": [
            "--number"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fraction",
          "flags": [
            "--fraction"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "bootstrap",
          "flags": [
            "--bootstrap"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "subsampled",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/alignment_subsample.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "ancestral_state_reconstruction",
      "handler": "ancestral_state_reconstruction",
      "aliases": [
        "anc_recon",
        "asr"
      ],
      "entry_points": [
        "pk_ancestral_state_reconstruction",
        "pk_anc_recon",
        "pk_asr"
      ],
      "title": "Ancestral state reconstruction",
      "summary": "Reconstruct ancestral character states",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/ancestral_state_reconstruction.rst",
      "documentation": {
        "purpose": "Reconstruct ancestral character states",
        "use_cases": [
          "Reconstruct ancestral character states"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait",
          "flags": [
            "-c",
            "--trait"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "type",
          "flags": [
            "--type"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "continuous",
          "choices": [
            "continuous",
            "discrete"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "-m",
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "fast",
          "choices": [
            "fast",
            "ml"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "model",
          "flags": [
            "--model"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "ER",
          "choices": [
            "ER",
            "SYM",
            "ARD"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "ci",
          "flags": [
            "--ci"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_ci",
          "flags": [
            "--plot-ci"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "ci_size",
          "flags": [
            "--ci-size"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 1.0,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/ancestral_state_reconstruction.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "bipartition_support_stats",
      "handler": "bipartition_support_stats",
      "aliases": [
        "bss"
      ],
      "entry_points": [
        "pk_bipartition_support_stats",
        "pk_bss"
      ],
      "title": "Bipartition support statistics",
      "summary": "Summary statistics of bipartition support values",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/bipartition_support_stats.rst",
      "documentation": {
        "purpose": "Summary statistics of bipartition support values",
        "use_cases": [
          "Summary statistics of bipartition support values"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "thresholds",
          "flags": [
            "--thresholds"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/bipartition_support_stats.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "branch_length_multiplier",
      "handler": "branch_length_multiplier",
      "aliases": [
        "blm"
      ],
      "entry_points": [
        "pk_branch_length_multiplier",
        "pk_blm"
      ],
      "title": "Branch length multiplier",
      "summary": "Multiply branch lengths by a factor",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/branch_length_multiplier.rst",
      "documentation": {
        "purpose": "Multiply branch lengths by a factor",
        "use_cases": [
          "Multiply branch lengths by a factor"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "factor",
          "flags": [
            "-f",
            "--factor"
          ],
          "positional": false,
          "required": true,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/branch_length_multiplier.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "character_map",
      "handler": "character_map",
      "aliases": [
        "charmap",
        "synapomorphy_map"
      ],
      "entry_points": [
        "pk_character_map",
        "pk_charmap",
        "pk_synapomorphy_map"
      ],
      "title": "Character map (synapomorphy/homoplasy mapping)",
      "summary": "Map synapomorphies and homoplasies onto a phylogeny",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/character_map.rst",
      "documentation": {
        "purpose": "Map synapomorphies and homoplasies onto a phylogeny",
        "use_cases": [
          "Map synapomorphies and homoplasies onto a phylogeny"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "data",
          "flags": [
            "-d",
            "--data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "optimization",
          "flags": [
            "--optimization"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "acctran",
          "choices": [
            "acctran",
            "deltran"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "phylogram",
          "flags": [
            "--phylogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "characters",
          "flags": [
            "--characters"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "allow_taxon_mismatch",
          "flags": [
            "--allow-taxon-mismatch"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "change_marker_size",
          "flags": [
            "--change-marker-size"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "change_fontsize",
          "flags": [
            "--change-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/character_map.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "chronogram",
      "handler": "chronogram",
      "aliases": [
        "chrono",
        "time_tree"
      ],
      "entry_points": [
        "pk_chronogram",
        "pk_chrono",
        "pk_time_tree"
      ],
      "title": "Chronogram",
      "summary": "Time-calibrated tree with geological timescale (rectangular or circular)",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/chronogram.rst",
      "documentation": {
        "purpose": "Time-calibrated tree with geological timescale (rectangular or circular)",
        "use_cases": [
          "Time-calibrated tree with geological timescale (rectangular or circular)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "root_age",
          "flags": [
            "--root-age"
          ],
          "positional": false,
          "required": true,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "timescale",
          "flags": [
            "--timescale"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "auto",
          "choices": [
            "auto",
            "epoch",
            "period",
            "era"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "node_ages",
          "flags": [
            "--node-ages"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/chronogram.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "codon_dnds",
      "handler": "codon_dnds",
      "aliases": [
        "dn_ds",
        "dnds",
        "kaks"
      ],
      "entry_points": [
        "pk_codon_dnds",
        "pk_dn_ds",
        "pk_dnds",
        "pk_kaks"
      ],
      "title": "Codon dN/dS",
      "summary": "Pairwise synonymous and nonsynonymous substitution-rate estimates",
      "categories": [
        "Alignment quality & statistics",
        "Evolutionary rate analysis"
      ],
      "page": "reference/commands/codon_dnds.rst",
      "documentation": {
        "purpose": "Pairwise synonymous and nonsynonymous substitution-rate estimates",
        "use_cases": [
          "Pairwise synonymous and nonsynonymous substitution-rate estimates"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "upper",
          "nargs": null,
          "default": "NG86",
          "choices": [
            "NG86",
            "LWL85",
            "YN00",
            "ML"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "genetic_code",
          "flags": [
            "--genetic-code"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 1,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "kappa",
          "flags": [
            "--kappa"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 1.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "codon_frequency",
          "flags": [
            "--codon-frequency"
          ],
          "positional": false,
          "required": false,
          "type": "upper",
          "nargs": null,
          "default": "F3X4",
          "choices": [
            "F1X4",
            "F3X4",
            "F61"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "stop_policy",
          "flags": [
            "--stop-policy"
          ],
          "positional": false,
          "required": false,
          "type": "string",
          "nargs": null,
          "default": "error",
          "choices": [
            "error",
            "skip"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "reference",
          "flags": [
            "--reference"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/codon_dnds.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "collapse_branches",
      "handler": "collapse_branches",
      "aliases": [
        "cb",
        "collapse"
      ],
      "entry_points": [
        "pk_collapse_branches",
        "pk_cb",
        "pk_collapse"
      ],
      "title": "Collapse bipartitions",
      "summary": "Collapse low-support bipartitions",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/collapse_branches.rst",
      "documentation": {
        "purpose": "Collapse low-support bipartitions",
        "use_cases": [
          "Collapse low-support bipartitions"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "support",
          "flags": [
            "-s",
            "--support"
          ],
          "positional": false,
          "required": true,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/collapse_branches.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "column_score",
      "handler": "column_score",
      "aliases": [
        "cs"
      ],
      "entry_points": [
        "pk_column_score",
        "pk_cs"
      ],
      "title": "Column score",
      "summary": "Column score for alignment quality",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/column_score.rst",
      "documentation": {
        "purpose": "Column score for alignment quality",
        "use_cases": [
          "Column score for alignment quality"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "fasta",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "reference",
          "flags": [
            "-r",
            "--reference"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/column_score.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "composition_per_taxon",
      "handler": "composition_per_taxon",
      "aliases": [
        "comp_tax",
        "comp_taxon"
      ],
      "entry_points": [
        "pk_composition_per_taxon",
        "pk_comp_tax",
        "pk_comp_taxon"
      ],
      "title": "Composition per taxon",
      "summary": "Nucleotide or amino acid composition per taxon",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/composition_per_taxon.rst",
      "documentation": {
        "purpose": "Nucleotide or amino acid composition per taxon",
        "use_cases": [
          "Nucleotide or amino acid composition per taxon"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/composition_per_taxon.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "compositional_bias_per_site",
      "handler": "compositional_bias_per_site",
      "aliases": [
        "cbps",
        "comp_bias_per_site"
      ],
      "entry_points": [
        "pk_compositional_bias_per_site",
        "pk_cbps",
        "pk_comp_bias_per_site"
      ],
      "title": "Compositional bias per site",
      "summary": "Detect compositional bias across sites",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/compositional_bias_per_site.rst",
      "documentation": {
        "purpose": "Detect compositional bias across sites",
        "use_cases": [
          "Detect compositional bias across sites"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "compositional_bias_per_site_plot.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/compositional_bias_per_site.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "concordance_asr",
      "handler": "concordance_asr",
      "aliases": [
        "casr",
        "conc_asr"
      ],
      "entry_points": [
        "pk_concordance_asr",
        "pk_casr",
        "pk_conc_asr"
      ],
      "title": "Concordance-aware ancestral state reconstruction",
      "summary": "ASR incorporating gene tree discordance",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/concordance_asr.rst",
      "documentation": {
        "purpose": "ASR incorporating gene tree discordance",
        "use_cases": [
          "ASR incorporating gene tree discordance"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait",
          "flags": [
            "-c",
            "--trait"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "-m",
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "weighted",
          "choices": [
            "weighted",
            "distribution"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "ci",
          "flags": [
            "--ci"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_uncertainty",
          "flags": [
            "--plot-uncertainty"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "missing_taxa",
          "flags": [
            "--missing-taxa"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "shared",
          "choices": [
            "error",
            "shared"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/concordance_asr.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "consensus_network",
      "handler": "consensus_network",
      "aliases": [
        "consnet",
        "splitnet",
        "splits_network"
      ],
      "entry_points": [
        "pk_consensus_network",
        "pk_consnet",
        "pk_splitnet",
        "pk_splits_network"
      ],
      "title": "Consensus network",
      "summary": "Consensus network from multiple trees",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/consensus_network.rst",
      "documentation": {
        "purpose": "Consensus network from multiple trees",
        "use_cases": [
          "Consensus network from multiple trees"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "trees",
          "flags": [
            "-t",
            "--trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "threshold",
          "flags": [
            "--threshold"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.1,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "missing_taxa",
          "flags": [
            "--missing-taxa"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "allow",
          "choices": [
            "allow",
            "error",
            "shared"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "max_splits",
          "flags": [
            "--max-splits"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 30,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "histogram",
          "flags": [
            "--histogram"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/consensus_network.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "consensus_tree",
      "handler": "consensus_tree",
      "aliases": [
        "consensus",
        "ctree"
      ],
      "entry_points": [
        "pk_consensus_tree",
        "pk_consensus",
        "pk_ctree"
      ],
      "title": "Consensus tree",
      "summary": "Consensus tree from multiple trees",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/consensus_tree.rst",
      "documentation": {
        "purpose": "Consensus tree from multiple trees",
        "use_cases": [
          "Consensus tree from multiple trees"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "trees",
          "flags": [
            "-t",
            "--trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "-m",
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "majority",
          "choices": [
            "strict",
            "majority"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "missing_taxa",
          "flags": [
            "--missing-taxa"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "error",
          "choices": [
            "error",
            "shared"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/consensus_tree.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "cont_map",
      "handler": "cont_map",
      "aliases": [
        "cmap",
        "contmap"
      ],
      "entry_points": [
        "pk_cont_map",
        "pk_cmap",
        "pk_contmap"
      ],
      "title": "Continuous trait mapping (contMap)",
      "summary": "Map continuous traits onto a phylogeny",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/cont_map.rst",
      "documentation": {
        "purpose": "Map continuous traits onto a phylogeny",
        "use_cases": [
          "Map continuous traits onto a phylogeny"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/cont_map.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "cophylo",
      "handler": "cophylo",
      "aliases": [
        "tangle",
        "tanglegram"
      ],
      "entry_points": [
        "pk_cophylo",
        "pk_tangle",
        "pk_tanglegram"
      ],
      "title": "Cophylogenetic plot (tanglegram)",
      "summary": "Tanglegram for comparing two trees",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/cophylo.rst",
      "documentation": {
        "purpose": "Tanglegram for comparing two trees",
        "use_cases": [
          "Tanglegram for comparing two trees"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree1",
          "flags": [
            "-t",
            "--tree1"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "tree2",
          "flags": [
            "-t2",
            "--tree2"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "mapping",
          "flags": [
            "-m",
            "--mapping"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/cophylo.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "covarying_evolutionary_rates",
      "handler": "covarying_evolutionary_rates",
      "aliases": [
        "cover"
      ],
      "entry_points": [
        "pk_covarying_evolutionary_rates",
        "pk_cover"
      ],
      "title": "Covarying evolutionary rates",
      "summary": "Detect covariation in evolutionary rates",
      "categories": [
        "Evolutionary rate analysis"
      ],
      "page": "reference/commands/covarying_evolutionary_rates.rst",
      "documentation": {
        "purpose": "Detect covariation in evolutionary rates",
        "use_cases": [
          "Detect covariation in evolutionary rates"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree_zero",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tree_one",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "reference",
          "flags": [
            "-r",
            "--reference"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "covarying_rates_plot.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/covarying_evolutionary_rates.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "create_concatenation_matrix",
      "handler": "create_concatenation_matrix",
      "aliases": [
        "cc",
        "create_concat"
      ],
      "entry_points": [
        "pk_create_concatenation_matrix",
        "pk_cc",
        "pk_create_concat"
      ],
      "title": "Create concatenation matrix",
      "summary": "Concatenate multiple alignments into a supermatrix",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/create_concatenation_matrix.rst",
      "documentation": {
        "purpose": "Concatenate multiple alignments into a supermatrix",
        "use_cases": [
          "Concatenate multiple alignments into a supermatrix"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment_list",
          "flags": [
            "-a",
            "--alignment",
            "--alignment-list",
            "--alignment_list"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "prefix",
          "flags": [
            "-p",
            "--prefix"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "threshold",
          "flags": [
            "--threshold"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "plot_occupancy",
          "flags": [
            "--plot-occupancy"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/create_concatenation_matrix.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "degree_of_violation_of_a_molecular_clock",
      "handler": "dvmc",
      "aliases": [
        "dvmc"
      ],
      "entry_points": [
        "pk_degree_of_violation_of_a_molecular_clock",
        "pk_dvmc"
      ],
      "title": "Degree of violation of the molecular clock",
      "summary": "Measure molecular clock violation",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/degree_of_violation_of_a_molecular_clock.rst",
      "documentation": {
        "purpose": "Measure molecular clock violation",
        "use_cases": [
          "Measure molecular clock violation"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/degree_of_violation_of_a_molecular_clock.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "density_map",
      "handler": "density_map",
      "aliases": [
        "densitymap",
        "dmap"
      ],
      "entry_points": [
        "pk_density_map",
        "pk_densitymap",
        "pk_dmap"
      ],
      "title": "Density map",
      "summary": "Posterior density of stochastic character maps",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/density_map.rst",
      "documentation": {
        "purpose": "Posterior density of stochastic character maps",
        "use_cases": [
          "Posterior density of stochastic character maps"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait",
          "flags": [
            "-c",
            "--trait"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "nsim",
          "flags": [
            "-n",
            "--nsim"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 100,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/density_map.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "dfoil",
      "handler": "dfoil",
      "aliases": [
        "dfoil_test"
      ],
      "entry_points": [
        "pk_dfoil",
        "pk_dfoil_test"
      ],
      "title": "DFOIL test (Pease & Hahn 2015)",
      "summary": "DFOIL test for detecting and polarizing introgression in a 5-taxon symmetric phylogeny",
      "categories": [
        "Introgression & gene flow"
      ],
      "page": "reference/commands/dfoil.rst",
      "documentation": {
        "purpose": "DFOIL test for detecting and polarizing introgression in a 5-taxon symmetric phylogeny",
        "use_cases": [
          "DFOIL test for detecting and polarizing introgression in a 5-taxon symmetric phylogeny"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "p1",
          "flags": [
            "--p1"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "p2",
          "flags": [
            "--p2"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "p3",
          "flags": [
            "--p3"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "p4",
          "flags": [
            "--p4"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "outgroup",
          "flags": [
            "--outgroup"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/dfoil.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "discordance_asymmetry",
      "handler": "discordance_asymmetry",
      "aliases": [
        "da",
        "disc_asym"
      ],
      "entry_points": [
        "pk_discordance_asymmetry",
        "pk_da",
        "pk_disc_asym"
      ],
      "title": "Discordance asymmetry",
      "summary": "Test for asymmetric discordance (gene flow detection)",
      "categories": [
        "Introgression & gene flow"
      ],
      "page": "reference/commands/discordance_asymmetry.rst",
      "documentation": {
        "purpose": "Test for asymmetric discordance (gene flow detection)",
        "use_cases": [
          "Test for asymmetric discordance (gene flow detection)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "annotate",
          "flags": [
            "--annotate"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/discordance_asymmetry.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "dstatistic",
      "handler": "dstatistic",
      "aliases": [
        "abba_baba",
        "dstat"
      ],
      "entry_points": [
        "pk_dstatistic",
        "pk_abba_baba",
        "pk_dstat"
      ],
      "title": "D-statistic (ABBA-BABA test)",
      "summary": "Patterson's D-statistic for detecting introgression",
      "categories": [
        "Introgression & gene flow"
      ],
      "page": "reference/commands/dstatistic.rst",
      "documentation": {
        "purpose": "Patterson's D-statistic for detecting introgression",
        "use_cases": [
          "Patterson's D-statistic for detecting introgression"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "p1",
          "flags": [
            "--p1"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "p2",
          "flags": [
            "--p2"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "p3",
          "flags": [
            "--p3"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "outgroup",
          "flags": [
            "--outgroup"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "block_size",
          "flags": [
            "--block-size"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 100,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "support",
          "flags": [
            "--support"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/dstatistic.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "dtt",
      "handler": "dtt",
      "aliases": [
        "disparity_through_time"
      ],
      "entry_points": [
        "pk_dtt",
        "pk_disparity_through_time"
      ],
      "title": "Disparity through time (DTT)",
      "summary": "Disparity-through-time analysis with MDI statistic (Harmon et al. 2003)",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/dtt.rst",
      "documentation": {
        "purpose": "Disparity-through-time analysis with MDI statistic (Harmon et al. 2003)",
        "use_cases": [
          "Disparity-through-time analysis with MDI statistic (Harmon et al. 2003)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "traits",
          "flags": [
            "--traits"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait",
          "flags": [
            "--trait"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "index",
          "flags": [
            "--index"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "avg_sq",
          "choices": [
            "avg_sq",
            "avg_manhattan"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "nsim",
          "flags": [
            "--nsim"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 0,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/dtt.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "evo_tempo_map",
      "handler": "evo_tempo_map",
      "aliases": [
        "etm"
      ],
      "entry_points": [
        "pk_evo_tempo_map",
        "pk_etm"
      ],
      "title": "Evolutionary tempo mapping",
      "summary": "Detect rate-topology associations in gene trees",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/evo_tempo_map.rst",
      "documentation": {
        "purpose": "Detect rate-topology associations in gene trees",
        "use_cases": [
          "Detect rate-topology associations in gene trees"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/evo_tempo_map.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "evolutionary_rate",
      "handler": "evolutionary_rate",
      "aliases": [
        "evo_rate"
      ],
      "entry_points": [
        "pk_evolutionary_rate",
        "pk_evo_rate"
      ],
      "title": "Evolutionary rate",
      "summary": "Calculate tree-based evolutionary rate",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/evolutionary_rate.rst",
      "documentation": {
        "purpose": "Calculate tree-based evolutionary rate",
        "use_cases": [
          "Calculate tree-based evolutionary rate"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/evolutionary_rate.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "evolutionary_rate_per_site",
      "handler": "evolutionary_rate_per_site",
      "aliases": [
        "erps",
        "evo_rate_per_site"
      ],
      "entry_points": [
        "pk_evolutionary_rate_per_site",
        "pk_erps",
        "pk_evo_rate_per_site"
      ],
      "title": "Evolutionary Rate per Site",
      "summary": "Site-specific evolutionary rate estimation",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/evolutionary_rate_per_site.rst",
      "documentation": {
        "purpose": "Site-specific evolutionary rate estimation",
        "use_cases": [
          "Site-specific evolutionary rate estimation"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "evolutionary_rate_per_site_plot.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/evolutionary_rate_per_site.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "faidx",
      "handler": "faidx",
      "aliases": [
        "ge",
        "get_entry"
      ],
      "entry_points": [
        "pk_faidx",
        "pk_ge",
        "pk_get_entry"
      ],
      "title": "Faidx",
      "summary": "Extract entries from FASTA files",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/faidx.rst",
      "documentation": {
        "purpose": "Extract entries from FASTA files",
        "use_cases": [
          "Extract entries from FASTA files"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "fasta",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "entry",
          "flags": [
            "-e",
            "--entry"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/faidx.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "faiths_pd",
      "handler": "faiths_pd",
      "aliases": [
        "faith_pd",
        "fpd",
        "phylo_diversity"
      ],
      "entry_points": [
        "pk_faiths_pd",
        "pk_faith_pd",
        "pk_fpd",
        "pk_phylo_diversity"
      ],
      "title": "Faith's phylogenetic diversity",
      "summary": "Sum of branch lengths spanning a community of tips",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/faiths_pd.rst",
      "documentation": {
        "purpose": "Sum of branch lengths spanning a community of tips",
        "use_cases": [
          "Sum of branch lengths spanning a community of tips"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "taxa",
          "flags": [
            "-t",
            "--taxa"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "exclude_root",
          "flags": [
            "--exclude-root"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/faiths_pd.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "fit_continuous",
      "handler": "fit_continuous",
      "aliases": [
        "fc",
        "fitcontinuous"
      ],
      "entry_points": [
        "pk_fit_continuous",
        "pk_fc",
        "pk_fitcontinuous"
      ],
      "title": "Continuous trait evolution model comparison (fitContinuous)",
      "summary": "Compare continuous trait evolution models (supports discordance-aware VCV with ``-g``)",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/fit_continuous.rst",
      "documentation": {
        "purpose": "Compare continuous trait evolution models (supports discordance-aware VCV with ``-g``)",
        "use_cases": [
          "Compare continuous trait evolution models (supports discordance-aware VCV with ``-g``)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "models",
          "flags": [
            "--models"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/fit_continuous.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "fit_discrete",
      "handler": "fit_discrete",
      "aliases": [
        "fd",
        "fitdiscrete"
      ],
      "entry_points": [
        "pk_fit_discrete",
        "pk_fd",
        "pk_fitdiscrete"
      ],
      "title": "Discrete trait evolution model comparison (fitDiscrete)",
      "summary": "Compare ER, SYM, ARD Mk models",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/fit_discrete.rst",
      "documentation": {
        "purpose": "Compare ER, SYM, ARD Mk models",
        "use_cases": [
          "Compare ER, SYM, ARD Mk models"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait",
          "flags": [
            "-c",
            "--trait"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "models",
          "flags": [
            "--models"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/fit_discrete.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "gc_content",
      "handler": "gc_content",
      "aliases": [
        "gc"
      ],
      "entry_points": [
        "pk_gc_content",
        "pk_gc"
      ],
      "title": "Guanine-cytosine (GC) content",
      "summary": "GC content of an alignment",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/gc_content.rst",
      "documentation": {
        "purpose": "GC content of an alignment",
        "use_cases": [
          "GC content of an alignment"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "fasta",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/gc_content.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "hidden_paralogy_check",
      "handler": "hidden_paralogy_check",
      "aliases": [
        "clan_check"
      ],
      "entry_points": [
        "pk_hidden_paralogy_check",
        "pk_clan_check"
      ],
      "title": "Hidden paralogy check",
      "summary": "Check for hidden paralogy in gene trees",
      "categories": [
        "Homology assessment"
      ],
      "page": "reference/commands/hidden_paralogy_check.rst",
      "documentation": {
        "purpose": "Check for hidden paralogy in gene trees",
        "use_cases": [
          "Check for hidden paralogy in gene trees"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "clade",
          "flags": [
            "-c",
            "--clade"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/hidden_paralogy_check.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "hybridization",
      "handler": "hybridization",
      "aliases": [
        "hybrid",
        "reticulation"
      ],
      "entry_points": [
        "pk_hybridization",
        "pk_hybrid",
        "pk_reticulation"
      ],
      "title": "Hybridization analysis",
      "summary": "Estimate reticulation events and localize hybridization on a species tree",
      "categories": [
        "Introgression & gene flow"
      ],
      "page": "reference/commands/hybridization.rst",
      "documentation": {
        "purpose": "Estimate reticulation events and localize hybridization on a species tree",
        "use_cases": [
          "Estimate reticulation events and localize hybridization on a species tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "support",
          "flags": [
            "--support"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "alpha",
          "flags": [
            "--alpha"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.05,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/hybridization.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "identity_matrix",
      "handler": "identity_matrix",
      "aliases": [
        "id_matrix",
        "seqid"
      ],
      "entry_points": [
        "pk_identity_matrix",
        "pk_id_matrix",
        "pk_seqid"
      ],
      "title": "Identity matrix",
      "summary": "Pairwise sequence identity heatmap",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/identity_matrix.rst",
      "documentation": {
        "purpose": "Pairwise sequence identity heatmap",
        "use_cases": [
          "Pairwise sequence identity heatmap"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "metric",
          "flags": [
            "--metric"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "identity",
          "choices": [
            "identity",
            "p-distance"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tree",
          "flags": [
            "--tree"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "sort",
          "flags": [
            "--sort"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "cluster",
          "choices": [
            "alpha",
            "cluster",
            "tree"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "partition",
          "flags": [
            "--partition"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/identity_matrix.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "independent_contrasts",
      "handler": "independent_contrasts",
      "aliases": [
        "phylo_contrasts",
        "pic"
      ],
      "entry_points": [
        "pk_independent_contrasts",
        "pk_phylo_contrasts",
        "pk_pic"
      ],
      "title": "Independent contrasts (PIC)",
      "summary": "Felsenstein's phylogenetically independent contrasts",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/independent_contrasts.rst",
      "documentation": {
        "purpose": "Felsenstein's phylogenetically independent contrasts",
        "use_cases": [
          "Felsenstein's phylogenetically independent contrasts"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/independent_contrasts.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "internal_branch_stats",
      "handler": "internal_branch_stats",
      "aliases": [
        "ibs"
      ],
      "entry_points": [
        "pk_internal_branch_stats",
        "pk_ibs"
      ],
      "title": "Internal branch statistics",
      "summary": "Summary statistics of internal branch lengths",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/internal_branch_stats.rst",
      "documentation": {
        "purpose": "Summary statistics of internal branch lengths",
        "use_cases": [
          "Summary statistics of internal branch lengths"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/internal_branch_stats.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "internode_labeler",
      "handler": "internode_labeler",
      "aliases": [
        "il"
      ],
      "entry_points": [
        "pk_internode_labeler",
        "pk_il"
      ],
      "title": "Internode labeler",
      "summary": "Label internal nodes of a tree",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/internode_labeler.rst",
      "documentation": {
        "purpose": "Label internal nodes of a tree",
        "use_cases": [
          "Label internal nodes of a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/internode_labeler.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "kf_distance",
      "handler": "kf_distance",
      "aliases": [
        "kf",
        "kf_dist",
        "kuhner_felsenstein_distance"
      ],
      "entry_points": [
        "pk_kf_distance",
        "pk_kf",
        "pk_kf_dist",
        "pk_kuhner_felsenstein_distance"
      ],
      "title": "Kuhner-Felsenstein distance",
      "summary": "Branch score distance between trees (topology + branch lengths)",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/kf_distance.rst",
      "documentation": {
        "purpose": "Branch score distance between trees (topology + branch lengths)",
        "use_cases": [
          "Branch score distance between trees (topology + branch lengths)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree_zero",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tree_one",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/kf_distance.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "last_common_ancestor_subtree",
      "handler": "last_common_ancestor_subtree",
      "aliases": [
        "lca_subtree"
      ],
      "entry_points": [
        "pk_last_common_ancestor_subtree",
        "pk_lca_subtree"
      ],
      "title": "Last common ancestor subtree",
      "summary": "Extract subtree from LCA of specified taxa",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/last_common_ancestor_subtree.rst",
      "documentation": {
        "purpose": "Extract subtree from LCA of specified taxa",
        "use_cases": [
          "Extract subtree from LCA of specified taxa"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "list_of_taxa",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/last_common_ancestor_subtree.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "long_branch_score",
      "handler": "lb_score",
      "aliases": [
        "lb_score",
        "lbs"
      ],
      "entry_points": [
        "pk_long_branch_score",
        "pk_lb_score",
        "pk_lbs"
      ],
      "title": "Long branch score",
      "summary": "Identify long branches in a tree",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/long_branch_score.rst",
      "documentation": {
        "purpose": "Identify long branches in a tree",
        "use_cases": [
          "Identify long branches in a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/long_branch_score.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "ltt",
      "handler": "ltt",
      "aliases": [
        "gamma",
        "gamma_stat"
      ],
      "entry_points": [
        "pk_ltt",
        "pk_gamma",
        "pk_gamma_stat"
      ],
      "title": "Lineage-through-time plot and gamma statistic",
      "summary": "Lineage-through-time analysis and gamma statistic",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/ltt.rst",
      "documentation": {
        "purpose": "Lineage-through-time analysis and gamma statistic",
        "use_cases": [
          "Lineage-through-time analysis and gamma statistic"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/ltt.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "mask_alignment",
      "handler": "mask_alignment",
      "aliases": [
        "mask",
        "mask_aln"
      ],
      "entry_points": [
        "pk_mask_alignment",
        "pk_mask",
        "pk_mask_aln"
      ],
      "title": "Mask alignment",
      "summary": "Mask sites in an alignment",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/mask_alignment.rst",
      "documentation": {
        "purpose": "Mask sites in an alignment",
        "use_cases": [
          "Mask sites in an alignment"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "max_gap",
          "flags": [
            "-g",
            "--max_gap"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 1.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "min_occupancy",
          "flags": [
            "-o",
            "--min_occupancy"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "max_entropy",
          "flags": [
            "-e",
            "--max_entropy"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/mask_alignment.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "monophyly_check",
      "handler": "monophyly_check",
      "aliases": [
        "is_monophyletic"
      ],
      "entry_points": [
        "pk_monophyly_check",
        "pk_is_monophyletic"
      ],
      "title": "Monophyly check",
      "summary": "Test monophyly of a group of taxa",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/monophyly_check.rst",
      "documentation": {
        "purpose": "Test monophyly of a group of taxa",
        "use_cases": [
          "Test monophyly of a group of taxa"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "list_of_taxa",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/monophyly_check.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "nearest_neighbor_interchange",
      "handler": "nearest_neighbor_interchange",
      "aliases": [
        "nni"
      ],
      "entry_points": [
        "pk_nearest_neighbor_interchange",
        "pk_nni"
      ],
      "title": "Nearest neighbor interchange",
      "summary": "Generate NNI tree rearrangements",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/nearest_neighbor_interchange.rst",
      "documentation": {
        "purpose": "Generate NNI tree rearrangements",
        "use_cases": [
          "Generate NNI tree rearrangements"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "branch",
          "flags": [
            "--branch"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "branches",
          "flags": [
            "--branches"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_input_tree",
          "flags": [
            "--no-input-tree"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/nearest_neighbor_interchange.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "neighbor_net",
      "handler": "neighbor_net",
      "aliases": [
        "nnet"
      ],
      "entry_points": [
        "pk_neighbor_net",
        "pk_nnet"
      ],
      "title": "NeighborNet",
      "summary": "NeighborNet phylogenetic network from distance matrix (Bryant & Moulton 2004)",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/neighbor_net.rst",
      "documentation": {
        "purpose": "NeighborNet phylogenetic network from distance matrix (Bryant & Moulton 2004)",
        "use_cases": [
          "NeighborNet phylogenetic network from distance matrix (Bryant & Moulton 2004)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "distance_matrix",
          "flags": [
            "--distance-matrix"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "metric",
          "flags": [
            "--metric"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "p-distance",
          "choices": [
            "identity",
            "p-distance",
            "jc"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "max_splits",
          "flags": [
            "--max-splits"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 30,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/neighbor_net.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "network_signal",
      "handler": "network_signal",
      "aliases": [
        "net_signal",
        "netsig"
      ],
      "entry_points": [
        "pk_network_signal",
        "pk_net_signal",
        "pk_netsig"
      ],
      "title": "Network signal",
      "summary": "Phylogenetic signal on networks",
      "categories": [
        "Phylogenetic signal"
      ],
      "page": "reference/commands/network_signal.rst",
      "documentation": {
        "purpose": "Phylogenetic signal on networks",
        "use_cases": [
          "Phylogenetic signal on networks"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait-data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "hybrid",
          "flags": [
            "--hybrid"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": "+",
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "quartet_json",
          "flags": [
            "--quartet-json"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "both",
          "choices": [
            "both",
            "blombergs_k",
            "lambda"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "permutations",
          "flags": [
            "--permutations"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 1000,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/network_signal.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "occupancy_filter",
      "handler": "occupancy_filter",
      "aliases": [
        "filter_occupancy",
        "occ_filter"
      ],
      "entry_points": [
        "pk_occupancy_filter",
        "pk_filter_occupancy",
        "pk_occ_filter"
      ],
      "title": "Occupancy filter",
      "summary": "Filter alignments or trees by cross-file taxon occupancy (works with both FASTA and Newick)",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/occupancy_filter.rst",
      "documentation": {
        "purpose": "Filter alignments or trees by cross-file taxon occupancy (works with both FASTA and Newick)",
        "use_cases": [
          "Filter alignments or trees by cross-file taxon occupancy (works with both FASTA and Newick)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "list",
          "flags": [
            "-l",
            "--list"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "format",
          "flags": [
            "-f",
            "--format"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "fasta",
          "choices": [
            "fasta",
            "trees"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "threshold",
          "flags": [
            "-t",
            "--threshold"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.5,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output_dir",
          "flags": [
            "-o",
            "--output-dir"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "suffix",
          "flags": [
            "--suffix"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": ".filtered",
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/occupancy_filter.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output-dir"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "occupancy_per_taxon",
      "handler": "occupancy_per_taxon",
      "aliases": [
        "occ_tax",
        "occupancy_taxon"
      ],
      "entry_points": [
        "pk_occupancy_per_taxon",
        "pk_occ_tax",
        "pk_occupancy_taxon"
      ],
      "title": "Occupancy per taxon",
      "summary": "Taxon occupancy in alignment columns",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/occupancy_per_taxon.rst",
      "documentation": {
        "purpose": "Taxon occupancy in alignment columns",
        "use_cases": [
          "Taxon occupancy in alignment columns"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/occupancy_per_taxon.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "ou_shift_detection",
      "handler": "ou_shift_detection",
      "aliases": [
        "detect_shifts",
        "l1ou",
        "ou_shifts"
      ],
      "entry_points": [
        "pk_ou_shift_detection",
        "pk_detect_shifts",
        "pk_l1ou",
        "pk_ou_shifts"
      ],
      "title": "OU shift detection (l1ou)",
      "summary": "Detect OU regime shifts on a phylogeny",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/ou_shift_detection.rst",
      "documentation": {
        "purpose": "Detect OU regime shifts on a phylogeny",
        "use_cases": [
          "Detect OU regime shifts on a phylogeny"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "criterion",
          "flags": [
            "--criterion"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "pBIC",
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "max_shifts",
          "flags": [
            "--max-shifts"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/ou_shift_detection.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "ouwie",
      "handler": "ouwie",
      "aliases": [
        "fit_ouwie",
        "multi_regime_ou"
      ],
      "entry_points": [
        "pk_ouwie",
        "pk_fit_ouwie",
        "pk_multi_regime_ou"
      ],
      "title": "Multi-regime OU models (OUwie)",
      "summary": "Multi-regime Ornstein-Uhlenbeck models",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/ouwie.rst",
      "documentation": {
        "purpose": "Multi-regime Ornstein-Uhlenbeck models",
        "use_cases": [
          "Multi-regime Ornstein-Uhlenbeck models"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "regime_data",
          "flags": [
            "-r",
            "--regime_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "models",
          "flags": [
            "--models"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/ouwie.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "pairwise_identity",
      "handler": "pairwise_identity",
      "aliases": [
        "pairwise_id",
        "pi"
      ],
      "entry_points": [
        "pk_pairwise_identity",
        "pk_pairwise_id",
        "pk_pi"
      ],
      "title": "Pairwise identity",
      "summary": "Pairwise sequence identity in an alignment",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/pairwise_identity.rst",
      "documentation": {
        "purpose": "Pairwise sequence identity in an alignment",
        "use_cases": [
          "Pairwise sequence identity in an alignment"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "exclude_gaps",
          "flags": [
            "-e",
            "--exclude_gaps"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "pairwise_identity_heatmap.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/pairwise_identity.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "parsimony_informative_sites",
      "handler": "parsimony_informative_sites",
      "aliases": [
        "pis"
      ],
      "entry_points": [
        "pk_parsimony_informative_sites",
        "pk_pis"
      ],
      "title": "Parsimony informative sites",
      "summary": "Count parsimony informative sites",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/parsimony_informative_sites.rst",
      "documentation": {
        "purpose": "Count parsimony informative sites",
        "use_cases": [
          "Count parsimony informative sites"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/parsimony_informative_sites.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "parsimony_score",
      "handler": "parsimony_score",
      "aliases": [
        "pars",
        "parsimony"
      ],
      "entry_points": [
        "pk_parsimony_score",
        "pk_pars",
        "pk_parsimony"
      ],
      "title": "Parsimony score",
      "summary": "Fitch parsimony score of a tree given an alignment",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/parsimony_score.rst",
      "documentation": {
        "purpose": "Fitch parsimony score of a tree given an alignment",
        "use_cases": [
          "Fitch parsimony score of a tree given an alignment"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/parsimony_score.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "patristic_distances",
      "handler": "patristic_distances",
      "aliases": [
        "pd"
      ],
      "entry_points": [
        "pk_patristic_distances",
        "pk_pd"
      ],
      "title": "Patristic distances",
      "summary": "Pairwise patristic distances between taxa",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/patristic_distances.rst",
      "documentation": {
        "purpose": "Pairwise patristic distances between taxa",
        "use_cases": [
          "Pairwise patristic distances between taxa"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/patristic_distances.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phenogram",
      "handler": "phenogram",
      "aliases": [
        "tg",
        "traitgram"
      ],
      "entry_points": [
        "pk_phenogram",
        "pk_tg",
        "pk_traitgram"
      ],
      "title": "Phenogram (traitgram)",
      "summary": "Phenogram visualizing trait evolution",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/phenogram.rst",
      "documentation": {
        "purpose": "Phenogram visualizing trait evolution",
        "use_cases": [
          "Phenogram visualizing trait evolution"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phenogram.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylo_anova",
      "handler": "phylo_anova",
      "aliases": [
        "panova",
        "phylo_manova",
        "pmanova"
      ],
      "entry_points": [
        "pk_phylo_anova",
        "pk_panova",
        "pk_phylo_manova",
        "pk_pmanova"
      ],
      "title": "Phylogenetic ANOVA / MANOVA",
      "summary": "Phylogenetic ANOVA or MANOVA using RRPP (Adams & Collyer 2018)",
      "categories": [
        "Phylogenetic comparative methods"
      ],
      "page": "reference/commands/phylo_anova.rst",
      "documentation": {
        "purpose": "Phylogenetic ANOVA or MANOVA using RRPP (Adams & Collyer 2018)",
        "use_cases": [
          "Phylogenetic ANOVA or MANOVA using RRPP (Adams & Collyer 2018)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "traits",
          "flags": [
            "--traits"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "group_column",
          "flags": [
            "--group-column"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "auto",
          "choices": [
            "auto",
            "anova",
            "manova"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "permutations",
          "flags": [
            "--permutations"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 1000,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "pairwise",
          "flags": [
            "--pairwise"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_type",
          "flags": [
            "--plot-type"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "auto",
          "choices": [
            "auto",
            "boxplot",
            "phylomorphospace"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylo_anova.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylo_gwas",
      "handler": "phylo_gwas",
      "aliases": [
        "pgwas"
      ],
      "entry_points": [
        "pk_phylo_gwas",
        "pk_pgwas"
      ],
      "title": "Phylo GWAS",
      "summary": "Phylogenetic genome-wide association study",
      "categories": [
        "Phylogenetic comparative methods"
      ],
      "page": "reference/commands/phylo_gwas.rst",
      "documentation": {
        "purpose": "Phylogenetic genome-wide association study",
        "use_cases": [
          "Phylogenetic genome-wide association study"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "phenotype",
          "flags": [
            "-d",
            "--phenotype"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "partition",
          "flags": [
            "-p",
            "--partition"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "alpha",
          "flags": [
            "--alpha"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.05,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "exclude_monophyletic",
          "flags": [
            "--exclude-monophyletic"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "dot_size",
          "flags": [
            "--dot-size"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 1.0,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "csv",
          "flags": [
            "--csv"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylo_gwas.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylo_heatmap",
      "handler": "phylo_heatmap",
      "aliases": [
        "ph",
        "pheatmap"
      ],
      "entry_points": [
        "pk_phylo_heatmap",
        "pk_ph",
        "pk_pheatmap"
      ],
      "title": "Phylogenetic heatmap",
      "summary": "Phylogeny alongside a heatmap of numeric trait values",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/phylo_heatmap.rst",
      "documentation": {
        "purpose": "Phylogeny alongside a heatmap of numeric trait values",
        "use_cases": [
          "Phylogeny alongside a heatmap of numeric trait values"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "data",
          "flags": [
            "-d",
            "--data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "split",
          "flags": [
            "--split"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.3,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "standardize",
          "flags": [
            "--standardize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cmap",
          "flags": [
            "--cmap"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "viridis",
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "cluster_columns",
          "flags": [
            "--cluster-columns"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylo_heatmap.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylo_impute",
      "handler": "phylo_impute",
      "aliases": [
        "impute",
        "phylo_imp"
      ],
      "entry_points": [
        "pk_phylo_impute",
        "pk_impute",
        "pk_phylo_imp"
      ],
      "title": "Phylogenetic imputation",
      "summary": "Impute missing trait values using phylogenetic relationships",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/phylo_impute.rst",
      "documentation": {
        "purpose": "Impute missing trait values using phylogenetic relationships",
        "use_cases": [
          "Impute missing trait values using phylogenetic relationships"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait-data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylo_impute.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylo_logistic",
      "handler": "phylo_logistic",
      "aliases": [
        "phylo_logreg",
        "plogreg"
      ],
      "entry_points": [
        "pk_phylo_logistic",
        "pk_phylo_logreg",
        "pk_plogreg"
      ],
      "title": "Phylogenetic Logistic Regression",
      "summary": "Phylogenetic logistic regression for binary traits (Ives & Garland 2010)",
      "categories": [
        "Phylogenetic comparative methods"
      ],
      "page": "reference/commands/phylo_logistic.rst",
      "documentation": {
        "purpose": "Phylogenetic logistic regression for binary traits (Ives & Garland 2010)",
        "use_cases": [
          "Phylogenetic logistic regression for binary traits (Ives & Garland 2010)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait-data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "response",
          "flags": [
            "--response"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "predictor",
          "flags": [
            "--predictor"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "logistic_MPLE",
          "choices": [
            "logistic_MPLE",
            "logistic_IG10"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylo_logistic.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylo_path",
      "handler": "phylo_path",
      "aliases": [
        "phylopath",
        "ppath"
      ],
      "entry_points": [
        "pk_phylo_path",
        "pk_phylopath",
        "pk_ppath"
      ],
      "title": "Phylogenetic path analysis",
      "summary": "Compare causal DAGs via d-separation + PGLS (von Hardenberg & Gonzalez-Voyer 2013)",
      "categories": [
        "Phylogenetic comparative methods"
      ],
      "page": "reference/commands/phylo_path.rst",
      "documentation": {
        "purpose": "Compare causal DAGs via d-separation + PGLS (von Hardenberg & Gonzalez-Voyer 2013)",
        "use_cases": [
          "Compare causal DAGs via d-separation + PGLS (von Hardenberg & Gonzalez-Voyer 2013)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "traits",
          "flags": [
            "--traits"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "models",
          "flags": [
            "--models"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "best_only",
          "flags": [
            "--best-only"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "csv",
          "flags": [
            "--csv"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylo_path.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylogenetic_glm",
      "handler": "phylogenetic_glm",
      "aliases": [
        "pglm",
        "phylo_glm"
      ],
      "entry_points": [
        "pk_phylogenetic_glm",
        "pk_pglm",
        "pk_phylo_glm"
      ],
      "title": "Phylogenetic GLM",
      "summary": "Phylogenetic generalized linear model (supports discordance-aware VCV with ``-g``)",
      "categories": [
        "Phylogenetic comparative methods"
      ],
      "page": "reference/commands/phylogenetic_glm.rst",
      "documentation": {
        "purpose": "Phylogenetic generalized linear model (supports discordance-aware VCV with ``-g``)",
        "use_cases": [
          "Phylogenetic generalized linear model (supports discordance-aware VCV with ``-g``)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "response",
          "flags": [
            "-y",
            "--response"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "predictors",
          "flags": [
            "-x",
            "--predictors"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": "+",
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "family",
          "flags": [
            "--family"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": [
            "binomial",
            "poisson"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": [
            "logistic_MPLE",
            "poisson_GEE"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "btol",
          "flags": [
            "--btol"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 10,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "log_alpha_bound",
          "flags": [
            "--log-alpha-bound"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 4,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylogenetic_glm.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylogenetic_ordination",
      "handler": "phylogenetic_ordination",
      "aliases": [
        "dimreduce",
        "ord",
        "ordination",
        "pdr",
        "phyl_pca",
        "phylo_dimreduce",
        "phylo_ordination",
        "phylo_pca",
        "ppca"
      ],
      "entry_points": [
        "pk_phylogenetic_ordination",
        "pk_dimreduce",
        "pk_ord",
        "pk_ordination",
        "pk_pdr",
        "pk_phyl_pca",
        "pk_phylo_dimreduce",
        "pk_phylo_ordination",
        "pk_phylo_pca",
        "pk_ppca"
      ],
      "title": "Phylogenetic Ordination",
      "summary": "Ordination incorporating phylogenetic structure (supports discordance-aware VCV with ``-g``)",
      "categories": [
        "Phylogenetic comparative methods"
      ],
      "page": "reference/commands/phylogenetic_ordination.rst",
      "documentation": {
        "purpose": "Ordination incorporating phylogenetic structure (supports discordance-aware VCV with ``-g``)",
        "use_cases": [
          "Ordination incorporating phylogenetic structure (supports discordance-aware VCV with ``-g``)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "pca",
          "choices": [
            "pca",
            "tsne",
            "umap"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "correction",
          "flags": [
            "--correction"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "BM",
          "choices": [
            "BM",
            "lambda"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "mode",
          "flags": [
            "--mode"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "cov",
          "choices": [
            "cov",
            "corr"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "n_components",
          "flags": [
            "--n-components"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 2,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "perplexity",
          "flags": [
            "--perplexity"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "n_neighbors",
          "flags": [
            "--n-neighbors"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "min_dist",
          "flags": [
            "--min-dist"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.1,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_tree",
          "flags": [
            "--plot-tree"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "no_plot_tree",
          "flags": [
            "--no-plot-tree"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_by",
          "flags": [
            "--color-by"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "tree_color_by",
          "flags": [
            "--tree-color-by"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "phylo_ordination_plot.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylogenetic_ordination.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylogenetic_regression",
      "handler": "phylogenetic_regression",
      "aliases": [
        "pgls",
        "phylo_regression"
      ],
      "entry_points": [
        "pk_phylogenetic_regression",
        "pk_pgls",
        "pk_phylo_regression"
      ],
      "title": "Phylogenetic regression (PGLS)",
      "summary": "Phylogenetic generalized least squares regression (supports discordance-aware VCV with ``-g``)",
      "categories": [
        "Phylogenetic comparative methods"
      ],
      "page": "reference/commands/phylogenetic_regression.rst",
      "documentation": {
        "purpose": "Phylogenetic generalized least squares regression (supports discordance-aware VCV with ``-g``)",
        "use_cases": [
          "Phylogenetic generalized least squares regression (supports discordance-aware VCV with ``-g``)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "response",
          "flags": [
            "-y",
            "--response"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "predictors",
          "flags": [
            "-x",
            "--predictors"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": "+",
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "-m",
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "BM",
          "choices": [
            "BM",
            "lambda"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylogenetic_regression.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "phylogenetic_signal",
      "handler": "phylogenetic_signal",
      "aliases": [
        "phylo_signal",
        "ps"
      ],
      "entry_points": [
        "pk_phylogenetic_signal",
        "pk_phylo_signal",
        "pk_ps"
      ],
      "title": "Phylogenetic signal",
      "summary": "Test for phylogenetic signal in traits (supports discordance-aware VCV with ``-g``)",
      "categories": [
        "Phylogenetic signal"
      ],
      "page": "reference/commands/phylogenetic_signal.rst",
      "documentation": {
        "purpose": "Test for phylogenetic signal in traits (supports discordance-aware VCV with ``-g``)",
        "use_cases": [
          "Test for phylogenetic signal in traits (supports discordance-aware VCV with ``-g``)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "-m",
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "blombergs_k",
          "choices": [
            "blombergs_k",
            "lambda"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "permutations",
          "flags": [
            "-p",
            "--permutations"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 1000,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "multivariate",
          "flags": [
            "--multivariate"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylogenetic_signal.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": [
            {
              "K": 0.584216001752301,
              "p_value": 0.474,
              "permutations": 1000,
              "r_squared_phylo": 0.9499081827368852
            },
            {
              "lambda": 0.9999933893038647,
              "log_likelihood": -11.569678737014614,
              "p_value": 0.7165426341460481,
              "r_squared_phylo": 0.9499081827368852
            },
            {
              "K": 0.5842,
              "p_value": 0.474,
              "permutations": 1000,
              "r_squared_phylo": 0.9499
            },
            {
              "K": 0.5819,
              "p_value": 0.479,
              "permutations": 1000,
              "r_squared_phylo": 0.9511,
              "vcv_metadata": {
                "n_gene_trees": 10,
                "n_shared_taxa": 8,
                "psd_corrected": false
              }
            }
          ]
        }
      }
    },
    {
      "canonical": "phylomorphospace",
      "handler": "phylomorphospace",
      "aliases": [
        "phmo",
        "phylomorpho"
      ],
      "entry_points": [
        "pk_phylomorphospace",
        "pk_phmo",
        "pk_phylomorpho"
      ],
      "title": "Phylomorphospace",
      "summary": "Phylomorphospace visualization",
      "categories": [
        "Phylogenetic comparative methods"
      ],
      "page": "reference/commands/phylomorphospace.rst",
      "documentation": {
        "purpose": "Phylomorphospace visualization",
        "use_cases": [
          "Phylomorphospace visualization"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_x",
          "flags": [
            "--trait-x"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_y",
          "flags": [
            "--trait-y"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "color_by",
          "flags": [
            "--color-by"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "phylomorphospace_plot.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/phylomorphospace.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "plot_alignment_qc",
      "handler": "plot_alignment_qc",
      "aliases": [
        "paqc",
        "plot_qc"
      ],
      "entry_points": [
        "pk_plot_alignment_qc",
        "pk_paqc",
        "pk_plot_qc"
      ],
      "title": "Plot alignment QC",
      "summary": "Visual quality control plots for alignments",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/plot_alignment_qc.rst",
      "documentation": {
        "purpose": "Visual quality control plots for alignments",
        "use_cases": [
          "Visual quality control plots for alignments"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "alignment_qc.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "width",
          "flags": [
            "--width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 14.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "height",
          "flags": [
            "--height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 10.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "gap_z",
          "flags": [
            "--gap-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "composition_z",
          "flags": [
            "--composition-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "distance_z",
          "flags": [
            "--distance-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "rcvt_z",
          "flags": [
            "--rcvt-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "occupancy_z",
          "flags": [
            "--occupancy-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "entropy_z",
          "flags": [
            "--entropy-z"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 3.0,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/plot_alignment_qc.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "polytomy_test",
      "handler": "polytomy_test",
      "aliases": [
        "polyt",
        "polyt_test",
        "ptt"
      ],
      "entry_points": [
        "pk_polytomy_test",
        "pk_polyt",
        "pk_polyt_test",
        "pk_ptt"
      ],
      "title": "Polytomy testing",
      "summary": "Test for polytomies in a tree",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/polytomy_test.rst",
      "documentation": {
        "purpose": "Test for polytomies in a tree",
        "use_cases": [
          "Test for polytomies in a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "trees",
          "flags": [
            "-t",
            "--trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "groups",
          "flags": [
            "-g",
            "--groups"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/polytomy_test.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "print_tree",
      "handler": "print_tree",
      "aliases": [
        "print",
        "pt"
      ],
      "entry_points": [
        "pk_print_tree",
        "pk_print",
        "pk_pt"
      ],
      "title": "Print tree",
      "summary": "Print ASCII representation of a tree",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/print_tree.rst",
      "documentation": {
        "purpose": "Print ASCII representation of a tree",
        "use_cases": [
          "Print ASCII representation of a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "remove",
          "flags": [
            "-r",
            "--remove"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/print_tree.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "prune_tree",
      "handler": "prune_tree",
      "aliases": [
        "prune"
      ],
      "entry_points": [
        "pk_prune_tree",
        "pk_prune"
      ],
      "title": "Prune tree",
      "summary": "Prune taxa from a tree",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/prune_tree.rst",
      "documentation": {
        "purpose": "Prune taxa from a tree",
        "use_cases": [
          "Prune taxa from a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "list_of_taxa",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "keep",
          "flags": [
            "-k",
            "--keep"
          ],
          "positional": false,
          "required": false,
          "type": "str2bool",
          "nargs": "?",
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ignore_branch_labels",
          "flags": [
            "--ignore-branch-labels"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/prune_tree.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "quartet_network",
      "handler": "quartet_network",
      "aliases": [
        "nanuq",
        "qnet",
        "quartet_net"
      ],
      "entry_points": [
        "pk_quartet_network",
        "pk_nanuq",
        "pk_qnet",
        "pk_quartet_net"
      ],
      "title": "Quartet network",
      "summary": "Quartet-based network visualization",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/quartet_network.rst",
      "documentation": {
        "purpose": "Quartet-based network visualization",
        "use_cases": [
          "Quartet-based network visualization"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "trees",
          "flags": [
            "-t",
            "--trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "alpha",
          "flags": [
            "--alpha"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.05,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "beta",
          "flags": [
            "--beta"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.95,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "missing_taxa",
          "flags": [
            "--missing-taxa"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "error",
          "choices": [
            "error",
            "shared"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/quartet_network.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "quartet_pie",
      "handler": "quartet_pie",
      "aliases": [
        "qpie",
        "quartet_pie_chart"
      ],
      "entry_points": [
        "pk_quartet_pie",
        "pk_qpie",
        "pk_quartet_pie_chart"
      ],
      "title": "Quartet pie chart",
      "summary": "Phylogram with quartet concordance pie charts at internal nodes",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/quartet_pie.rst",
      "documentation": {
        "purpose": "Phylogram with quartet concordance pie charts at internal nodes",
        "use_cases": [
          "Phylogram with quartet concordance pie charts at internal nodes"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "annotate",
          "flags": [
            "--annotate"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "branch_labels",
          "flags": [
            "--branch-labels"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "csv",
          "flags": [
            "--csv"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "pie_size",
          "flags": [
            "--pie-size"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 1.0,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/quartet_pie.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "rate_heterogeneity",
      "handler": "rate_heterogeneity",
      "aliases": [
        "brownie",
        "rh"
      ],
      "entry_points": [
        "pk_rate_heterogeneity",
        "pk_brownie",
        "pk_rh"
      ],
      "title": "Rate heterogeneity test (multi-rate Brownian motion)",
      "summary": "Test for rate heterogeneity in trait evolution",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/rate_heterogeneity.rst",
      "documentation": {
        "purpose": "Test for rate heterogeneity in trait evolution",
        "use_cases": [
          "Test for rate heterogeneity in trait evolution"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "regime_data",
          "flags": [
            "-r",
            "--regime_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "nsim",
          "flags": [
            "-n",
            "--nsim"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 0,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/rate_heterogeneity.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "relative_composition_variability",
      "handler": "rcv",
      "aliases": [
        "rcv",
        "rel_comp_var"
      ],
      "entry_points": [
        "pk_relative_composition_variability",
        "pk_rcv",
        "pk_rel_comp_var"
      ],
      "title": "Relative composition variability",
      "summary": "Composition variability across taxa",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/relative_composition_variability.rst",
      "documentation": {
        "purpose": "Composition variability across taxa",
        "use_cases": [
          "Composition variability across taxa"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/relative_composition_variability.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "relative_composition_variability_taxon",
      "handler": "rcvt",
      "aliases": [
        "rcvt",
        "rel_comp_var_taxon"
      ],
      "entry_points": [
        "pk_relative_composition_variability_taxon",
        "pk_rcvt",
        "pk_rel_comp_var_taxon"
      ],
      "title": "Relative composition variability, taxon",
      "summary": "Per-taxon relative composition variability",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/relative_composition_variability_taxon.rst",
      "documentation": {
        "purpose": "Per-taxon relative composition variability",
        "use_cases": [
          "Per-taxon relative composition variability"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "rcvt_plot.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/relative_composition_variability_taxon.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "relative_rate_test",
      "handler": "relative_rate_test",
      "aliases": [
        "rrt",
        "tajima_rrt"
      ],
      "entry_points": [
        "pk_relative_rate_test",
        "pk_rrt",
        "pk_tajima_rrt"
      ],
      "title": "Relative rate test",
      "summary": "Relative rate test between lineages",
      "categories": [
        "Evolutionary rate analysis"
      ],
      "page": "reference/commands/relative_rate_test.rst",
      "documentation": {
        "purpose": "Relative rate test between lineages",
        "use_cases": [
          "Relative rate test between lineages"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "alignment_list",
          "flags": [
            "-l",
            "--alignment-list"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/relative_rate_test.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "rename_fasta_entries",
      "handler": "rename_fasta_entries",
      "aliases": [
        "rename_fasta"
      ],
      "entry_points": [
        "pk_rename_fasta_entries",
        "pk_rename_fasta"
      ],
      "title": "Rename FASTA entries",
      "summary": "Rename entries in a FASTA file",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/rename_fasta_entries.rst",
      "documentation": {
        "purpose": "Rename entries in a FASTA file",
        "use_cases": [
          "Rename entries in a FASTA file"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "fasta",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "idmap",
          "flags": [
            "-i",
            "--idmap"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/rename_fasta_entries.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "rename_tree_tips",
      "handler": "rename_tree_tips",
      "aliases": [
        "rename_tips",
        "rename_tree"
      ],
      "entry_points": [
        "pk_rename_tree_tips",
        "pk_rename_tips",
        "pk_rename_tree"
      ],
      "title": "Rename tree tips",
      "summary": "Rename tip labels in a tree",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/rename_tree_tips.rst",
      "documentation": {
        "purpose": "Rename tip labels in a tree",
        "use_cases": [
          "Rename tip labels in a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "idmap",
          "flags": [
            "-i",
            "--idmap"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/rename_tree_tips.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "robinson_foulds_distance",
      "handler": "rf_distance",
      "aliases": [
        "rf",
        "rf_dist",
        "rf_distance"
      ],
      "entry_points": [
        "pk_robinson_foulds_distance",
        "pk_rf",
        "pk_rf_dist",
        "pk_rf_distance"
      ],
      "title": "Robinson-Foulds distance",
      "summary": "Topological distance between trees",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/robinson_foulds_distance.rst",
      "documentation": {
        "purpose": "Topological distance between trees",
        "use_cases": [
          "Topological distance between trees"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree_zero",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tree_one",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/robinson_foulds_distance.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "root_tree",
      "handler": "root_tree",
      "aliases": [
        "root",
        "rt"
      ],
      "entry_points": [
        "pk_root_tree",
        "pk_root",
        "pk_rt"
      ],
      "title": "Root tree",
      "summary": "Root or reroot a tree",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/root_tree.rst",
      "documentation": {
        "purpose": "Root or reroot a tree",
        "use_cases": [
          "Root or reroot a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "root",
          "flags": [
            "-r",
            "--root"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/root_tree.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "saturation",
      "handler": "saturation",
      "aliases": [
        "sat"
      ],
      "entry_points": [
        "pk_saturation",
        "pk_sat"
      ],
      "title": "Saturation",
      "summary": "Test for substitution saturation",
      "categories": [
        "Saturation & model adequacy"
      ],
      "page": "reference/commands/saturation.rst",
      "documentation": {
        "purpose": "Test for substitution saturation",
        "use_cases": [
          "Test for substitution saturation"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "exclude_gaps",
          "flags": [
            "-e",
            "--exclude_gaps"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "saturation_plot.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/saturation.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "simmap_summary",
      "handler": "simmap_summary",
      "aliases": [
        "describe_simmap",
        "smsummary"
      ],
      "entry_points": [
        "pk_simmap_summary",
        "pk_describe_simmap",
        "pk_smsummary"
      ],
      "title": "SIMMAP summary",
      "summary": "Per-branch SIMMAP summary with node posteriors (describe.simmap)",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/simmap_summary.rst",
      "documentation": {
        "purpose": "Per-branch SIMMAP summary with node posteriors (describe.simmap)",
        "use_cases": [
          "Per-branch SIMMAP summary with node posteriors (describe.simmap)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait",
          "flags": [
            "-c",
            "--trait"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "model",
          "flags": [
            "-m",
            "--model"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "ER",
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "nsim",
          "flags": [
            "-n",
            "--nsim"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 100,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "csv",
          "flags": [
            "--csv"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/simmap_summary.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "spectral_discordance",
      "handler": "spectral_discordance",
      "aliases": [
        "sd",
        "spec_disc"
      ],
      "entry_points": [
        "pk_spectral_discordance",
        "pk_sd",
        "pk_spec_disc"
      ],
      "title": "Spectral discordance decomposition",
      "summary": "PCA ordination and clustering of gene tree topologies",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/spectral_discordance.rst",
      "documentation": {
        "purpose": "PCA ordination and clustering of gene tree topologies",
        "use_cases": [
          "PCA ordination and clustering of gene tree topologies"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "metric",
          "flags": [
            "--metric"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "nrf",
          "choices": [
            "nrf",
            "wrf"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "clusters",
          "flags": [
            "--clusters"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "n_pcs",
          "flags": [
            "--n-pcs"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "top_loadings",
          "flags": [
            "--top-loadings"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 5,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/spectral_discordance.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "spurious_sequence",
      "handler": "spurious_sequence",
      "aliases": [
        "spurious_seq",
        "ss"
      ],
      "entry_points": [
        "pk_spurious_sequence",
        "pk_spurious_seq",
        "pk_ss"
      ],
      "title": "Spurious homolog identification",
      "summary": "Detect long-branch and high-diameter-impact sequence outliers",
      "categories": [
        "Homology assessment"
      ],
      "page": "reference/commands/spurious_sequence.rst",
      "documentation": {
        "purpose": "Identify sequence outliers from terminal branch lengths or their impact on weighted tree diameter",
        "use_cases": [
          "Screen one gene tree for unusually long terminal branches",
          "Detect tips that disproportionately increase a gene tree's diameter",
          "Calibrate diameter-impact signatures across many genes or separately by species"
        ],
        "input_formats": [
          "A single Newick tree for median-factor or per-gene diameter-impact analysis",
          "With --tree-list, a line-delimited file of Newick tree paths; blank and comment lines are ignored"
        ],
        "outputs": [
          "Median-factor TSV rows: taxon, terminal branch length, threshold, and median",
          "Diameter-impact TSV rows: optional tree path, taxon, signature, p-value, removal rank, terminal branch length, and before/after diameters",
          "With --json, metadata and candidate rows in a structured object"
        ],
        "errors": [
          "Diameter-impact analysis rejects trees with fewer than four tips or missing, negative, or non-finite branch lengths",
          "Diameter-impact-only options cannot be combined with median-factor analysis",
          "--per-species requires --tree-list"
        ],
        "limitations": [
          "Reported tips are candidates for review; the command does not edit alignments or trees",
          "The diameter-impact method is a deterministic TreeShrink-inspired endpoint-removal heuristic, not TreeShrink's full optimal removal-set search",
          "Per-species groups with fewer than four observations are not called as outliers"
        ],
        "scientific_interpretation": "A larger diameter-impact signature means that removing the tip causes a larger proportional decrease in weighted tree diameter; a tip is reported only when its one-sided tail probability is below --alpha.",
        "validation": [
          "Newick parsing requires one tree with unique, nonblank tip labels",
          "Diameter-impact analysis requires at least four tips and finite, nonnegative lengths on every non-root branch",
          "--alpha must be finite and between 0 and 1; --max-remove must leave at least two tips"
        ],
        "citations": [
          "Shen et al. 2018, Cell, doi:10.1016/j.cell.2018.10.023",
          "Mai and Mirarab 2018, BMC Genomics 19:272, doi:10.1186/s12864-018-4620-2"
        ],
        "examples": [
          "phykit spurious_sequence gene.tre --factor 20",
          "phykit spurious_sequence gene.tre --method diameter-impact --alpha 0.05",
          "phykit spurious_sequence trees.txt --method diameter-impact --tree-list --per-species --json"
        ],
        "related_commands": [
          "hidden_paralogy_check",
          "long_branch_score",
          "terminal_branch_stats"
        ],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "factor",
          "flags": [
            "-f",
            "--factor"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "string",
          "nargs": null,
          "default": "median-factor",
          "choices": [
            "median-factor",
            "diameter-impact"
          ],
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "alpha",
          "flags": [
            "--alpha"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.05,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "max_remove",
          "flags": [
            "--max-remove"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tree_list",
          "flags": [
            "--tree-list"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "per_species",
          "flags": [
            "--per-species"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/spurious_sequence.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": [
            {
              "alpha": 0.05,
              "method": "diameter-impact",
              "rows": [
                {
                  "diameter_after": 2.0,
                  "diameter_before": 101.0,
                  "p_value": 7e-06,
                  "removal_rank": 1,
                  "signature": 3.921973,
                  "taxon": "outlier",
                  "terminal_branch_length": 100.0,
                  "tree": "gene.tre"
                }
              ],
              "scope": "per-gene",
              "spurious_sequences": [
                {
                  "diameter_after": 2.0,
                  "diameter_before": 101.0,
                  "p_value": 7e-06,
                  "removal_rank": 1,
                  "signature": 3.921973,
                  "taxon": "outlier",
                  "terminal_branch_length": 100.0,
                  "tree": "gene.tre"
                }
              ],
              "tree_count": 1
            }
          ]
        }
      }
    },
    {
      "canonical": "stochastic_character_map",
      "handler": "stochastic_character_map",
      "aliases": [
        "scm",
        "simmap"
      ],
      "entry_points": [
        "pk_stochastic_character_map",
        "pk_scm",
        "pk_simmap"
      ],
      "title": "Stochastic character mapping (SIMMAP)",
      "summary": "Stochastic character mapping on a phylogeny",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/stochastic_character_map.rst",
      "documentation": {
        "purpose": "Stochastic character mapping on a phylogeny",
        "use_cases": [
          "Stochastic character mapping on a phylogeny"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait",
          "flags": [
            "-c",
            "--trait"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "model",
          "flags": [
            "-m",
            "--model"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "ER",
          "choices": [
            "ER",
            "SYM",
            "ARD"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "nsim",
          "flags": [
            "-n",
            "--nsim"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 100,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/stochastic_character_map.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "subtree_prune_regraft",
      "handler": "subtree_prune_regraft",
      "aliases": [
        "spr"
      ],
      "entry_points": [
        "pk_subtree_prune_regraft",
        "pk_spr"
      ],
      "title": "Subtree pruning and regrafting",
      "summary": "Generate all SPR rearrangements for a specified subtree",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/subtree_prune_regraft.rst",
      "documentation": {
        "purpose": "Generate all SPR rearrangements for a specified subtree",
        "use_cases": [
          "Generate all SPR rearrangements for a specified subtree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "subtree",
          "flags": [
            "--subtree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/subtree_prune_regraft.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "sum_of_pairs_score",
      "handler": "sum_of_pairs_score",
      "aliases": [
        "sop",
        "sops"
      ],
      "entry_points": [
        "pk_sum_of_pairs_score",
        "pk_sop",
        "pk_sops"
      ],
      "title": "Sum-of-pairs score",
      "summary": "Sum-of-pairs alignment quality score",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/sum_of_pairs_score.rst",
      "documentation": {
        "purpose": "Sum-of-pairs alignment quality score",
        "use_cases": [
          "Sum-of-pairs alignment quality score"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "fasta",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "reference",
          "flags": [
            "-r",
            "--reference"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/sum_of_pairs_score.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "taxon_groups",
      "handler": "taxon_groups",
      "aliases": [
        "shared_taxa",
        "tgroups"
      ],
      "entry_points": [
        "pk_taxon_groups",
        "pk_shared_taxa",
        "pk_tgroups"
      ],
      "title": "Taxon groups",
      "summary": "Group alignment or tree files by shared taxon sets (works with both FASTA and Newick)",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/taxon_groups.rst",
      "documentation": {
        "purpose": "Group alignment or tree files by shared taxon sets (works with both FASTA and Newick)",
        "use_cases": [
          "Group alignment or tree files by shared taxon sets (works with both FASTA and Newick)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "list",
          "flags": [
            "-l",
            "--list"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "format",
          "flags": [
            "-f",
            "--format"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "trees",
          "choices": [
            "trees",
            "fasta"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/taxon_groups.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "terminal_branch_stats",
      "handler": "terminal_branch_stats",
      "aliases": [
        "tbs"
      ],
      "entry_points": [
        "pk_terminal_branch_stats",
        "pk_tbs"
      ],
      "title": "Terminal branch statistics",
      "summary": "Summary statistics of terminal branch lengths",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/terminal_branch_stats.rst",
      "documentation": {
        "purpose": "Summary statistics of terminal branch lengths",
        "use_cases": [
          "Summary statistics of terminal branch lengths"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "verbose",
          "flags": [
            "-v",
            "--verbose"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/terminal_branch_stats.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "thread_dna",
      "handler": "thread_dna",
      "aliases": [
        "p2n",
        "pal2nal"
      ],
      "entry_points": [
        "pk_thread_dna",
        "pk_p2n",
        "pk_pal2nal"
      ],
      "title": "Protein-to-nucleotide alignment",
      "summary": "Thread nucleotide onto protein alignment",
      "categories": [
        "Alignment & dataset utilities"
      ],
      "page": "reference/commands/thread_dna.rst",
      "documentation": {
        "purpose": "Thread nucleotide onto protein alignment",
        "use_cases": [
          "Thread nucleotide onto protein alignment"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "protein",
          "flags": [
            "-p",
            "--protein"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "nucleotide",
          "flags": [
            "-n",
            "--nucleotide"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "clipkit_log_file",
          "flags": [
            "-c",
            "--clipkit-log-file",
            "--clipkit_log_file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "stop",
          "flags": [
            "-s",
            "--stop"
          ],
          "positional": false,
          "required": false,
          "type": "str2bool",
          "nargs": "?",
          "default": true,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/thread_dna.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "threshold_model",
      "handler": "threshold_model",
      "aliases": [
        "thresh",
        "thresh_bayes",
        "threshbayes",
        "threshold"
      ],
      "entry_points": [
        "pk_threshold_model",
        "pk_thresh",
        "pk_thresh_bayes",
        "pk_threshbayes",
        "pk_threshold"
      ],
      "title": "Threshold model",
      "summary": "Felsenstein threshold model for trait correlation",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/threshold_model.rst",
      "documentation": {
        "purpose": "Felsenstein threshold model for trait correlation",
        "use_cases": [
          "Felsenstein threshold model for trait correlation"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait-data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "traits",
          "flags": [
            "--traits"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "types",
          "flags": [
            "--types"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ngen",
          "flags": [
            "--ngen"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 100000,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "sample",
          "flags": [
            "--sample"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 100,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "burnin",
          "flags": [
            "--burnin"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.2,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/threshold_model.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "tip_labels",
      "handler": "tip_labels",
      "aliases": [
        "labels",
        "tl",
        "tree_labels"
      ],
      "entry_points": [
        "pk_tip_labels",
        "pk_labels",
        "pk_tl",
        "pk_tree_labels"
      ],
      "title": "Tip labels",
      "summary": "Print tip labels of a tree",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/tip_labels.rst",
      "documentation": {
        "purpose": "Print tip labels of a tree",
        "use_cases": [
          "Print tip labels of a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/tip_labels.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "tip_to_tip_distance",
      "handler": "tip_to_tip_distance",
      "aliases": [
        "t2t",
        "t2t_dist"
      ],
      "entry_points": [
        "pk_tip_to_tip_distance",
        "pk_t2t",
        "pk_t2t_dist"
      ],
      "title": "Tip-to-tip distance",
      "summary": "Distance between two tips in a tree",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/tip_to_tip_distance.rst",
      "documentation": {
        "purpose": "Distance between two tips in a tree",
        "use_cases": [
          "Distance between two tips in a tree"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree_zero",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tip_1",
          "flags": [],
          "positional": true,
          "required": false,
          "type": "str",
          "nargs": "?",
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tip_2",
          "flags": [],
          "positional": true,
          "required": false,
          "type": "str",
          "nargs": "?",
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "all_pairs",
          "flags": [
            "--all-pairs"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot",
          "flags": [
            "--plot"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "plot_output",
          "flags": [
            "--plot-output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "tip_to_tip_distance_heatmap.png",
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/tip_to_tip_distance.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--plot-output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "tip_to_tip_node_distance",
      "handler": "tip_to_tip_node_distance",
      "aliases": [
        "t2t_nd",
        "t2t_node_dist"
      ],
      "entry_points": [
        "pk_tip_to_tip_node_distance",
        "pk_t2t_nd",
        "pk_t2t_node_dist"
      ],
      "title": "Tip-to-tip node distance",
      "summary": "Node distance between two tips",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/tip_to_tip_node_distance.rst",
      "documentation": {
        "purpose": "Node distance between two tips",
        "use_cases": [
          "Node distance between two tips"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree_zero",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tip_1",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "tip_2",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/tip_to_tip_node_distance.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "total_tree_length",
      "handler": "total_tree_length",
      "aliases": [
        "tree_len"
      ],
      "entry_points": [
        "pk_total_tree_length",
        "pk_tree_len"
      ],
      "title": "Total tree length",
      "summary": "Sum of all branch lengths",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/total_tree_length.rst",
      "documentation": {
        "purpose": "Sum of all branch lengths",
        "use_cases": [
          "Sum of all branch lengths"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/total_tree_length.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "trait_correlation",
      "handler": "trait_correlation",
      "aliases": [
        "phylo_corr",
        "trait_corr"
      ],
      "entry_points": [
        "pk_trait_correlation",
        "pk_phylo_corr",
        "pk_trait_corr"
      ],
      "title": "Trait correlation",
      "summary": "Phylogenetic correlations between all pairs of traits with heatmap visualization",
      "categories": [
        "Phylogenetic signal"
      ],
      "page": "reference/commands/trait_correlation.rst",
      "documentation": {
        "purpose": "Phylogenetic correlations between all pairs of traits with heatmap visualization",
        "use_cases": [
          "Phylogenetic correlations between all pairs of traits with heatmap visualization"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait-data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "alpha",
          "flags": [
            "--alpha"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": 0.05,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "cluster",
          "flags": [
            "--cluster"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "gene_trees",
          "flags": [
            "-g",
            "--gene-trees"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/trait_correlation.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "trait_rate_map",
      "handler": "trait_rate_map",
      "aliases": [
        "branch_rates",
        "rate_map"
      ],
      "entry_points": [
        "pk_trait_rate_map",
        "pk_branch_rates",
        "pk_rate_map"
      ],
      "title": "Trait rate map",
      "summary": "Per-branch evolutionary rate map for a continuous trait",
      "categories": [
        "Trait evolution"
      ],
      "page": "reference/commands/trait_rate_map.rst",
      "documentation": {
        "purpose": "Per-branch evolutionary rate map for a continuous trait",
        "use_cases": [
          "Per-branch evolutionary rate map for a continuous trait"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait_data",
          "flags": [
            "-d",
            "--trait_data"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "trait",
          "flags": [
            "--trait"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/trait_rate_map.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "transfer_annotations",
      "handler": "transfer_annotations",
      "aliases": [
        "annotate_tree",
        "transfer_annot"
      ],
      "entry_points": [
        "pk_transfer_annotations",
        "pk_annotate_tree",
        "pk_transfer_annot"
      ],
      "title": "Transfer annotations",
      "summary": "Transfer node annotations between trees (e.g., wASTRAL to RAxML/IQ-TREE)",
      "categories": [
        "Tree manipulation & utilities"
      ],
      "page": "reference/commands/transfer_annotations.rst",
      "documentation": {
        "purpose": "Transfer node annotations between trees (e.g., wASTRAL to RAxML/IQ-TREE)",
        "use_cases": [
          "Transfer node annotations between trees (e.g., wASTRAL to RAxML/IQ-TREE)"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "source",
          "flags": [
            "--source"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "target",
          "flags": [
            "--target"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/transfer_annotations.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "tree_space",
      "handler": "tree_space",
      "aliases": [
        "tree_landscape",
        "tspace"
      ],
      "entry_points": [
        "pk_tree_space",
        "pk_tree_landscape",
        "pk_tspace"
      ],
      "title": "Tree space visualization",
      "summary": "Visualize gene tree topology space via MDS, t-SNE, UMAP, or clustered distance heatmap",
      "categories": [
        "Tree comparison & consensus"
      ],
      "page": "reference/commands/tree_space.rst",
      "documentation": {
        "purpose": "Visualize gene tree topology space via MDS, t-SNE, UMAP, or clustered distance heatmap",
        "use_cases": [
          "Visualize gene tree topology space via MDS, t-SNE, UMAP, or clustered distance heatmap"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "trees",
          "flags": [
            "-t",
            "--trees"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "output",
          "flags": [
            "-o",
            "--output"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "metric",
          "flags": [
            "--metric"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "rf",
          "choices": [
            "rf",
            "kf"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "method",
          "flags": [
            "--method"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": "mds",
          "choices": [
            "mds",
            "tsne",
            "umap"
          ],
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "species_tree",
          "flags": [
            "--species-tree"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "k",
          "flags": [
            "--k"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "seed",
          "flags": [
            "--seed"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "heatmap",
          "flags": [
            "--heatmap"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "distance_matrix",
          "flags": [
            "--distance-matrix"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "fig_width",
          "flags": [
            "--fig-width"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "fig_height",
          "flags": [
            "--fig-height"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "dpi",
          "flags": [
            "--dpi"
          ],
          "positional": false,
          "required": false,
          "type": "int",
          "nargs": null,
          "default": 300,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "no_title",
          "flags": [
            "--no-title"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "title",
          "flags": [
            "--title"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "legend_position",
          "flags": [
            "--legend-position"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ylabel_fontsize",
          "flags": [
            "--ylabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "xlabel_fontsize",
          "flags": [
            "--xlabel-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "title_fontsize",
          "flags": [
            "--title-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "axis_fontsize",
          "flags": [
            "--axis-fontsize"
          ],
          "positional": false,
          "required": false,
          "type": "float",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "colors",
          "flags": [
            "--colors"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "ladderize",
          "flags": [
            "--ladderize"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "cladogram",
          "flags": [
            "--cladogram"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "circular",
          "flags": [
            "--circular"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        },
        {
          "name": "color_file",
          "flags": [
            "--color-file"
          ],
          "positional": false,
          "required": false,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/tree_space.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [
          "--output"
        ],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "treeness",
      "handler": "treeness",
      "aliases": [
        "tness"
      ],
      "entry_points": [
        "pk_treeness",
        "pk_tness"
      ],
      "title": "Treeness",
      "summary": "Ratio of internal to total branch lengths",
      "categories": [
        "Tree summary statistics"
      ],
      "page": "reference/commands/treeness.rst",
      "documentation": {
        "purpose": "Ratio of internal to total branch lengths",
        "use_cases": [
          "Ratio of internal to total branch lengths"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "tree",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/treeness.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "treeness_over_rcv",
      "handler": "treeness_over_rcv",
      "aliases": [
        "tor",
        "toverr"
      ],
      "entry_points": [
        "pk_treeness_over_rcv",
        "pk_tor",
        "pk_toverr"
      ],
      "title": "Treeness over RCV",
      "summary": "Treeness over relative composition variability",
      "categories": [
        "Saturation & model adequacy"
      ],
      "page": "reference/commands/treeness_over_rcv.rst",
      "documentation": {
        "purpose": "Treeness over relative composition variability",
        "use_cases": [
          "Treeness over relative composition variability"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [
            "-a",
            "--alignment"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "tree",
          "flags": [
            "-t",
            "--tree"
          ],
          "positional": false,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": "",
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/treeness_over_rcv.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "variable_sites",
      "handler": "variable_sites",
      "aliases": [
        "vs"
      ],
      "entry_points": [
        "pk_variable_sites",
        "pk_vs"
      ],
      "title": "Variable sites",
      "summary": "Count variable sites in an alignment",
      "categories": [
        "Alignment quality & statistics"
      ],
      "page": "reference/commands/variable_sites.rst",
      "documentation": {
        "purpose": "Count variable sites in an alignment",
        "use_cases": [
          "Count variable sites in an alignment"
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [
        {
          "name": "alignment",
          "flags": [],
          "positional": true,
          "required": true,
          "type": "str",
          "nargs": null,
          "default": null,
          "choices": null,
          "metavar": null,
          "action": "_StoreAction"
        },
        {
          "name": "json",
          "flags": [
            "--json"
          ],
          "positional": false,
          "required": false,
          "type": "boolean",
          "nargs": 0,
          "default": false,
          "choices": null,
          "metavar": null,
          "action": "_StoreTrueAction"
        }
      ],
      "documentation_url": "reference/commands/variable_sites.html",
      "output_contract": {
        "stdout": "Structured JSON with --json; otherwise command-specific text or data.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": true,
          "schema": {
            "$schema": "https://json-schema.org/draft/2020-12/schema",
            "type": [
              "object",
              "array"
            ],
            "description": "Command-specific fields are documented on the canonical page and in checked examples."
          },
          "examples": []
        }
      }
    },
    {
      "canonical": "version",
      "handler": "version",
      "aliases": [
        "v"
      ],
      "entry_points": [
        "pk_version",
        "pk_v"
      ],
      "title": "Version",
      "summary": "Run the Version analysis or utility.",
      "categories": [
        "Other utilities"
      ],
      "page": "reference/commands/version.rst",
      "documentation": {
        "purpose": "Run the Version analysis or utility.",
        "use_cases": [
          "Run the Version analysis or utility."
        ],
        "input_formats": [],
        "outputs": [],
        "errors": [],
        "limitations": [],
        "scientific_interpretation": "See the canonical command page.",
        "validation": [],
        "citations": [],
        "examples": [],
        "related_commands": [],
        "related_tutorials": []
      },
      "arguments": [],
      "documentation_url": "reference/commands/version.html",
      "output_contract": {
        "stdout": "Command-specific text or data; see the canonical page.",
        "stderr": "Diagnostics and warnings; invalid command syntax exits with status 2.",
        "file_options": [],
        "json": {
          "available": false,
          "schema": null,
          "examples": []
        }
      }
    }
  ]
}
