Alignment length

Length of an input alignment

Command identity

Canonical command:

alignment_length

Handler:

alignment_length

Aliases:

al, aln_len

Standalone executables:

pk_alignment_length, pk_al, pk_aln_len

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit alignment_length <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

Length of an input alignment is calculated using this function.

Longer alignments are associated with a strong phylogenetic signal.

The association between alignment length and phylogenetic signal was determined by Shen et al., Genome Biology and Evolution (2016), doi: 10.1093/gbe/evw179.

phykit aln_len <alignment> [--json]

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