Variable sites

Count variable sites in an alignment

Command identity

Canonical command:

variable_sites

Handler:

variable_sites

Aliases:

vs

Standalone executables:

pk_variable_sites, pk_vs

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit variable_sites <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 the number of variable sites in an alignment.

The number of variable sites in an alignment is associated with a strong phylogenetic signal.

PhyKIT reports three tab delimited values: col1: number of variable sites col2: total number of sites col3: percentage of variable sites

The association between the number of variable sites and phylogenetic signal was determined by Shen et al., Genome Biology and Evolution (2016), doi: 10.1093/gbe/evw179.

phykit variable_sites <alignment> [--json]

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