Taxon groups

Group alignment or tree files by shared taxon sets (works with both FASTA and Newick)

Command identity

Canonical command:

taxon_groups

Handler:

taxon_groups

Aliases:

shared_taxa, tgroups

Standalone executables:

pk_taxon_groups, pk_shared_taxa, pk_tgroups

Categories:

Alignment & dataset utilities

Runtime interface

Synopsis

phykit taxon_groups --list <list> [--format <format>] [--json]

Arguments

This table is generated from the live command parser. It is the authoritative source for accepted spellings, required arguments, types, defaults, and choices.

Argument	Required	Type	Default	Choices
-l, --list	true	str	required	any
-f, --format	false	str	trees	trees, fasta
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Unless the guidance below states otherwise, results are emitted as command output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Determine which tree or FASTA files share the same set of taxa. Reads a file listing paths to gene trees or alignments and groups them by their taxon set (exact match). Reports groups sorted by size (largest first), with the taxa present in each group.

Useful for identifying subsets of genes with identical taxon sampling for concatenation or comparative analysis.

phykit taxon_groups -l <file> [-f trees|fasta] [--json]

Options:
-l/--list: file listing paths to gene trees or FASTA files (one per line). Blank lines and lines starting with # are skipped. Relative paths are resolved relative to the list file's directory.
-f/--format: input format: trees (Newick) or fasta (FASTA alignment). Default: trees.
--json: optional argument to print results as JSON