Relative composition variability

Composition variability across taxa

Command identity

Canonical command:

relative_composition_variability

Handler:

rcv

Aliases:

rcv, rel_comp_var

Standalone executables:

pk_relative_composition_variability, pk_rcv, pk_rel_comp_var

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit relative_composition_variability <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 RCV (relative composition variability) for an alignment.

Lower RCV values are thought to be desirable because they represent a lower composition bias in an alignment. Statistically, RCV describes the average variability in sequence composition among taxa.

RCV is calculated following Phillips and Penny, Molecular Phylogenetics and Evolution (2003), doi: 10.1016/S1055-7903(03)00057-5.

RCV calculations are case-insensitive. Gap and ambiguous characters are excluded from composition counts and correction terms, and each taxon is normalized by its valid (non-excluded) sequence length.

phykit relative_composition_variability <alignment> [--json]

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