pseqsid1.1.0

Feed pseqsid a protein multiple-sequence alignment in FASTA format, and it produces CSV matrices of pairwise identity, similarity, or normalized similarity scores (NSS). This command-line program, developed and maintained by Amaury Pupo Meriño, compares every aligned protein entry with the others.

The --identity option measures identical residues at equivalent positions as a percentage of the selected sequence length, while --similarity also counts residues classified as similar. The --nss option calculates a pairwise Normalized Similarity Score using substitution-based log-odds values. With --length, users can choose the smallest, mean, largest, or full alignment length when gaps occur; gap-only columns are excluded from the first three choices but included in the alignment length. Similarity groups are supplied with --grouping, and if that option is omitted with --similarity, pseqsid creates and uses default_aa_similarity_groups.txt.

The grouping file uses a group-name colon followed by single-letter amino-acid codes, allows each group name only once, and assigns each amino acid to no more than one group; a # character begins a comment. Only standard amino acids and the hyphen gap character are accepted, so DNA alignments are interpreted as proteins and produce meaningless similarity and NSS results.

pseqsid is open-source Linux education software suited to students, instructors, and researchers analyzing protein conservation or alignment relationships from the command line. Version 1.1.0 requires Linux with snapd and runs on x86_64 (amd64) systems.