Phylo GWAS

Phylogenetic genome-wide association study

Command identity

Canonical command:

phylo_gwas

Handler:

phylo_gwas

Aliases:

pgwas

Standalone executables:

pk_phylo_gwas, pk_pgwas

Categories:

Phylogenetic comparative methods

Runtime interface

Synopsis

phykit phylo_gwas --alignment <alignment> --phenotype <phenotype> --output <output> [--tree <tree>] [--partition <partition>] [--alpha <alpha>] [--exclude-monophyletic] [--dot-size <dot_size>] [--csv <csv>] [--fig-width <fig_width>] [--fig-height <fig_height>] [--dpi <dpi>] [--no-title] [--title <title>] [--legend-position <legend_position>] [--ylabel-fontsize <ylabel_fontsize>] [--xlabel-fontsize <xlabel_fontsize>] [--title-fontsize <title_fontsize>] [--axis-fontsize <axis_fontsize>] [--colors <colors>] [--ladderize] [--cladogram] [--circular] [--color-file <color_file>] [--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
-a, --alignment	true	str	required	any
-d, --phenotype	true	str	required	any
-o, --output	true	str	required	any
-t, --tree	false	str	none	any
-p, --partition	false	str	none	any
--alpha	false	float	0.05	any
--exclude-monophyletic	false	boolean	false	any
--dot-size	false	float	1.0	any
--csv	false	str	none	any
--fig-width	false	float	none	any
--fig-height	false	float	none	any
--dpi	false	int	300	any
--no-title	false	boolean	false	any
--title	false	str	none	any
--legend-position	false	str	none	any
--ylabel-fontsize	false	float	none	any
--xlabel-fontsize	false	float	none	any
--title-fontsize	false	float	none	any
--axis-fontsize	false	float	none	any
--colors	false	str	none	any
--ladderize	false	boolean	false	any
--cladogram	false	boolean	false	any
--circular	false	boolean	false	any
--color-file	false	str	none	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Output-file options: --output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Phylogenetic genome-wide association study following the Pease et al. (2016) approach. Performs per-site association tests between alignment columns and a phenotype, applies Benjamini-Hochberg FDR correction, optionally classifies significant associations as monophyletic or polyphyletic using a phylogenetic tree, and produces a Manhattan plot.

Categorical phenotypes use Fisher's exact test (2 groups) or chi-squared test (>2 groups). Continuous phenotypes use point-biserial correlation. Only biallelic sites are tested; invariant and multiallelic sites are skipped. Sites with gaps or ambiguous characters are also skipped.

phykit phylo_gwas -a <alignment> -d <phenotype> -o <output>
  [-t <tree>] [-p <partition>] [--alpha 0.05]
  [--exclude-monophyletic] [--csv <file>] [--json]

Options:
-a/--alignment: FASTA alignment file
-d/--phenotype: two-column TSV file (taxon<tab>phenotype)
-o/--output: output Manhattan plot path
-t/--tree: optional Newick tree for monophyletic/polyphyletic classification
-p/--partition: optional RAxML-style partition file for gene annotations
--alpha: FDR significance threshold (default: 0.05)
--exclude-monophyletic: exclude monophyletic associations from results
--dot-size: scale factor for dot size in the Manhattan plot (default: 1.0; use 2.0 for double, 0.5 for half)
--csv: output per-site results as CSV to the specified file
--fig-width: figure width in inches (auto-scaled if omitted)
--fig-height: figure height in inches (auto-scaled if omitted)
--dpi: resolution in DPI (default: 300)
--no-title: hide the plot title
--title: custom title text
--legend-position: legend location (e.g., "upper right", "none")
--colors: comma-separated colors (hex or named)
--json: optional argument to print results as JSON