Compositional bias per site

Detect compositional bias across sites

Command identity

Canonical command:

compositional_bias_per_site

Handler:

compositional_bias_per_site

Aliases:

cbps, comp_bias_per_site

Standalone executables:

pk_compositional_bias_per_site, pk_cbps, pk_comp_bias_per_site

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit compositional_bias_per_site <alignment> [--plot] [--plot-output <plot_output>] [--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
alignment	true	str	required	any
--plot	false	boolean	false	any
--plot-output	false	str	compositional_bias_per_site_plot.png	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: --plot-output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Calculates compositional bias per site in an alignment.

Site-wise chi-squared tests are conducted in an alignment to detect compositional biases. PhyKIT outputs four columns:
col 1: index in alignment
col 2: chi-squared statistic (higher values indicate greater bias)
col 3: multi-test corrected p-value (Benjamini-Hochberg false discovery rate procedure)
col 4: uncorrected p-value

phykit comp_bias_per_site <alignment> [--plot] [--plot-output <path>]
        [--fig-width <float>] [--fig-height <float>] [--dpi <int>] [--no-title] [--title <str>]
        [--legend-position <str>] [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
        [--title-fontsize <float>] [--axis-fontsize <float>] [--colors <str>] [--ladderize] [--cladogram] [--circular] [--color-file <file>] [--json]

Options:
<alignment>: first argument after function name should be a query fasta alignment to calculate the site-wise compositional bias of
--plot: save a Manhattan-style plot of site-wise compositional bias
--plot-output: output path for plot (default: compositional_bias_per_site_plot.png)
--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" to hide)
--ylabel-fontsize: font size for y-axis labels; 0 to hide
--xlabel-fontsize: font size for x-axis labels; 0 to hide
--title-fontsize: font size for the title
--axis-fontsize: font size for axis labels
--colors: comma-separated colors (hex or named)
--ladderize: ladderize (sort) the tree before plotting
--cladogram: draw cladogram (equal branch lengths, tips aligned) instead of phylogram
--circular: draw circular (radial/fan) phylogram instead of rectangular
--color-file: color annotation file for tip labels, clade ranges, and branch colors (iTOL-inspired TSV format)
--json: optional argument to print results as JSON