Alignment length no gaps

Alignment length excluding gapped sites

Command identity

Canonical command:

alignment_length_no_gaps

Handler:

alignment_length_no_gaps

Aliases:

aln_len_no_gaps, alng

Standalone executables:

pk_alignment_length_no_gaps, pk_aln_len_no_gaps, pk_alng

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit alignment_length_no_gaps <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 alignment length excluding sites with gaps.

Longer alignments when excluding sites with gaps are associated with a strong phylogenetic signal.

PhyKIT reports three tab delimited values: col1: number of sites without gaps col2: total number of sites col3: percentage of sites without gaps

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

phykit aln_len_no_gaps <alignment> [--json]

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