Composition per taxon

Nucleotide or amino acid composition per taxon

Command identity

Canonical command:

composition_per_taxon

Handler:

composition_per_taxon

Aliases:

comp_tax, comp_taxon

Standalone executables:

pk_composition_per_taxon, pk_comp_tax, pk_comp_taxon

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit composition_per_taxon <alignment> [--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
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Unless the guidance below states otherwise, results are emitted as command output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Calculate sequence composition per taxon in an alignment.

Composition is reported as semicolon-separated symbol:frequency pairs for each taxon. Frequencies are calculated from valid (non-gap/non-ambiguous) characters. Symbol order is alphabetical.

phykit composition_per_taxon <alignment> [--json]

Example output:

1       A:0.4;C:0.0;G:0.2;T:0.4
2       A:0.5;C:0.0;G:0.25;T:0.25

Options:
<alignment>: first argument after function name should be an alignment file
--json: optional argument to print results as JSON