esl-alipid(1)

✨ NAME ✨

esl-alipid — bestie, this one calculates pairwise percent identities for all the sequence pairs in an MSA 💖

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🦋 SYNOPSIS 🦋

esl-alipid [options] msafile

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🌸 DESCRIPTION 🌸

okay so esl-alistat calculates the pairwise percent identity of each sequence pair in in the MSA(s) in msafile. (yes, the page says esl-alistat right there, we're just relaying the vibes fr fr 💅)

For each sequence pair, it outputs a line of

<sqname1> <sqname2> <pid> <nid> <n>

where:

• <pid> is the percent identity,
• <nid> is the number of identical aligned pairs, and
• <n> is the denominator used for the calculation: the shorter of the two (unaligned) sequence lengths.

If msafile is - (a single dash, iconic behavior honestly), alignment input is read from stdin.

🚨 Only canonical residues are counted toward <nid> and <n>. Degenerate residue codes are not counted. no cap, that's just how it is 😭

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🎀 OPTIONS 🎀

• -h — Print brief help; includes version number and a summary of all the options, even the expert ones. the full tea ☕
• --informat <s> — Assert that input msafile is in alignment format <s>, bypassing format autodetection. Common choices for <s> include: stockholm, a2m, afa, psiblast, clustal, phylip. For more information, and for codes for some less common formats, see the main documentation. The string <s> is case-insensitive (a2m or A2M both work — she's flexible like that 💁‍♀️).
• --amino — Assert that the msafile contains protein sequences. 🧬
• --dna — Assert that the msafile contains DNA sequences. 🧬
• --rna — Assert that the msafile contains RNA sequences. 🧬

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💜 SEE ALSO 💜

http://bioeasel.org/ — go look, it's giving main character energy ⭐

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👑 COPYRIGHT 👑

Copyright (C) 2020 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license. slay 💅

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🌈 AUTHOR 🌈

http://eddylab.org

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that's the whole page bestie, you ate it up 🫶

Easel 0.48 — Nov 2020 — esl-alipid(1), and that's the vibe check, periodt ✨