Alignment entropy

Shannon entropy across alignment sites

Command identity

Canonical command:

alignment_entropy

Handler:

alignment_entropy

Aliases:

aln_entropy, entropy

Standalone executables:

pk_alignment_entropy, pk_aln_entropy, pk_entropy

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit alignment_entropy <alignment> [--verbose] [--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
-v, --verbose	false	boolean	false	any
--plot	false	boolean	false	any
--plot-output	false	str	alignment_entropy_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 alignment entropy.

Site-wise entropy is calculated using Shannon entropy. By default, PhyKIT reports the mean entropy across all sites in the alignment. With the -v/--verbose option, PhyKIT reports entropy for each site.

phykit alignment_entropy <alignment> [-v/--verbose] [--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]

Example output (default):

0.657

Example output (-v):

1       0.0
2       1.0
3       0.971

Options:
<alignment>: first argument after function name should be an alignment file
-v/--verbose: optional argument to print entropy for each site
--plot: save a per-site alignment entropy plot
--plot-output: output path for plot (default: alignment_entropy_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