Column score

Column score for alignment quality

Command identity

Canonical command:

column_score

Handler:

column_score

Aliases:

cs

Standalone executables:

pk_column_score, pk_cs

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit column_score <fasta> [--reference <reference>] [--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
fasta	true	str	required	any
-r, --reference	false	str	none	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

Calculates column score.

Column score is an accuracy metric for a multiple alignment relative to a reference alignment. It is calculated by summing the correctly aligned columns over all columns in an alignment. Thus, values range from 0 to 1 and higher values indicate more accurate alignments.

Column score is calculated following Thompson et al., Nucleic Acids Research (1999), doi: 10.1093/nar/27.13.2682.

phykit column_score <alignment> --reference <reference_alignment> [--json]

Options:
<alignment>: first argument after function name should be a query fasta alignment file to be scored for accuracy
-r/--reference: reference alignment to compare the query alignment to
--json: optional argument to print results as JSON