Sum-of-pairs score

Sum-of-pairs alignment quality score

Command identity

Canonical command:

sum_of_pairs_score

Handler:

sum_of_pairs_score

Aliases:

sop, sops

Standalone executables:

pk_sum_of_pairs_score, pk_sop, pk_sops

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit sum_of_pairs_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 sum-of-pairs score.

Sum-of-pairs is an accuracy metric for a multiple alignment relative to a reference alignment. It is calculated by summing the correctly aligned residue pairs over all pairs of sequences. Thus, values range from 0 to 1 and higher values indicate more accurate alignments.

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

phykit sum_of_pairs_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