COMPALIGN(1)

💖 COMPALIGN(1) — the compare-two-multiple-alignments girlie 💖

okay bestie, welcome to compalign, from the General Commands Manual section of your local man pages. this one is a bop, i promise. it's giving "i have two alignments and i need to know how much they agree" and honestly? iconic. ✨

🌸 NAME 🌸

compalign — compare two multiple alignments. that's it. that's the whole job. she compares. she aligns. she serves. 💅

🦋 SYNOPSIS 🦋

compalign [-options] <trusted-alignment> <test-alignment>

two files, bestie. one trusted, one test. she's gonna put them side by side and tell you how well they match. 🫶

✨ DESCRIPTION ✨

so here's the tea, and it's actual science tea:

compalign calculates the fractional "identity" between the trusted alignment and the test alignment. and listen — the two files must contain exactly the same sequences, in exactly the same order. no exceptions. no remixing. no "i sorted them alphabetically for you." same sequences, same order, periodt. 💀

The identity of the multiple sequence alignments is defined as the averaged identity over all N(N-1)/2 pairwise alignments. like, she checks every possible pair. every single one. she's thorough like that. 👑

and the fractional identity of two sets of pairwise alignments is in turn defined like this — for aligned known sequences k1 and k2, and aligned test sequences t1 and t2:

matched columns / total columns

where:

• total columns = the total number of columns in which there is a valid (nongap) symbol in k1 or k2;
• matched columns = the number of columns in which one of the following is true:
  1. k1 and k2 both have valid symbols at a given column; t1 and t2 have the same symbols aligned in a column of the t1/t2 alignment;
  2. k1 has a symbol aligned to a gap in k2; that symbol in t1 is also aligned to a gap;
  3. k2 has a symbol aligned to a gap in k1; that symbol in t2 is also aligned to a gap.

got it? it's a vibe check on your gaps. gaps that match up? matched. gaps that don't? not matched. it's giving accountability. 🌈

⚠️ heads up bestie: because scores for all possible pairs are calculated, the algorithm is of order (N^2)L for N sequences of length L. so like… large sequence sets will take a while. she's not slow, she's thorough. but fr fr, bring a snack. 🍓

🎀 OPTIONS 🎀

Available options, and yes we're going through every single one:

• -h — print short help and usage info. your lil "hi what do i type" button. 🫶
• -c — only compare under marked #=CS consensus structure. she'll stay in her lane and only look at the parts you flagged. 💅
• --informat <s> — specify that both alignments are in format <s> (MSF, for instance). so like, tell her what dialect they're speaking. 🗣️
• --quiet — suppress verbose header (used in regression testing). no chit-chat, just results. main character energy but silent. 🤫

🌟 SEE ALSO 🌟

the whole squad, all of them, no one left out: afetch(1), alistat(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1). go say hi. they're all family. 🦋

💜 AUTHOR 💜

Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu

This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others). ty for your service bestie 🫡💖

okay that's the whole page, and this lil sign-off is where the footer would've been: this one is dated Mon, 01 Aug 2005 15:28:08 -0300, and yeah, it's the COMPALIGN(1) page. now go compare some alignments and slay. ✨💅👑