Relative composition variability, taxon

Per-taxon relative composition variability

Command identity

Canonical command:

relative_composition_variability_taxon

Handler:

rcvt

Aliases:

rcvt, rel_comp_var_taxon

Standalone executables:

pk_relative_composition_variability_taxon, pk_rcvt, pk_rel_comp_var_taxon

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit relative_composition_variability_taxon <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	rcvt_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

Calculate RCVT (relative composition variability, taxon) for an alignment.

RCVT is the relative composition variability metric for individual taxa. This facilitates identifying specific taxa that may have compositional biases. Lower RCVT values are more desirable because they indicate a lower composition bias for a given taxon in an alignment.

RCVT calculations are case-insensitive and exclude gap/ambiguous symbols from composition counts and normalization.

phykit relative_composition_variability_taxon <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 an alignment file
--plot: optional argument to generate an RCVT per-taxon barplot
--plot-output: output path for the RCVT plot (default: rcvt_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