Evolutionary Rate per Site

Site-specific evolutionary rate estimation

Command identity

Canonical command:

evolutionary_rate_per_site

Handler:

evolutionary_rate_per_site

Aliases:

erps, evo_rate_per_site

Standalone executables:

pk_evolutionary_rate_per_site, pk_erps, pk_evo_rate_per_site

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit evolutionary_rate_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

evolutionary_rate_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

Estimate evolutionary rate per site.

Evolutionary rate per site is one minus the sum of squared frequency of different characters at a given site. Values may range from 0 (slow evolving; no diversity at the given site) to 1 (fast evolving; all characters appear only once).

phykit evo_rate_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 evolutionary rate of
--plot: save a per-site evolutionary-rate plot
--plot-output: output path for plot (default: evolutionary_rate_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