esl-weight(1)

📦
version 3.3.2 · 2 versions
, in fedora 43, fedora 44

💖 esl-weight(1) — the Easel manual, but make it cute 💖

okay bestie, so you found yourself in the Easel section of the man pages (that's manual page esl-weight(1), from the Easel Manual, iykyk) and you're like "what is this". don't worry. I got you. 🫶

✨ NAME ✨

esl-weight — calculate sequence weights in MSA(s). that's it, that's the whole job. 💅

🌸 SYNOPSIS 🌸

esl-weight [options] msafile

🦋 DESCRIPTION 🦋

so what esl-weight does is: it calculates individual sequence weights for each alignment inside msafile, and then it outputs a whole new multiple sequence alignment file in Stockholm format. and the weights? they get annotated in Stockholm-format #=GS seqname WT weight lines. yes, that's a real format. iconic of them.

the default weighting algorithm is the Gerstein/Sonnhammer/Chothia algorithm. so if you just run it with no options, that's the one you get. no cap.

and one lil detail that matters a lot: if msafile is - (a single dash, bestie, just one), then the MSA input is read from stdin. chef's kiss.

🎀 OPTIONS 🎀

  • -h — print brief help. and when I say brief help I mean it also gives you the version number and a summary of all the options, including the expert options. so honestly, start here.
  • -g — use the Gerstein/Sonnhammer/Chothia weighting algorithm. this is the default, so it's the one you already have. you're welcome.
  • -p — use the Henikoff position-based weighting algorithm. this one is faster and more memory efficient than the default. so if your alignment is giving big and your RAM is giving small, this is your girl.
  • -b — "BLOSUM weights": uses approximately the same rule that was used in constructing the BLOSUM score matrices. what does that mean? it involves single-linkage clustering at some fractional identity threshold (default 0.62; see the --id option, bestie), and then for each cluster, it splits a total weight of one uniformly amongst all sequences in the cluster. total weight of one per cluster, split evenly. that's the whole vibe.

🔥 EXPERT OPTIONS 🔥

  • --id <x> — sets the fractional identity threshold used by the BLOSUM weighting rule (that's option -b; and yes it's required for that rule, don't skip it) to a number 0<=x<=1. the default is 0.62.
  • --amino — assert that the msafile contains protein sequences.
  • --dna — assert that the msafile contains DNA sequences.
  • --rna — assert that the msafile contains RNA sequences.

💜 SEE ALSO 💜

go look. it's giving resources. ✨

Copyright (C) 2020 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license. slay, honestly.

🌈 AUTHOR 🌈

and that's the whole page, bestie!! this was Easel 0.48, from Nov 2020, and it's the esl-weight(1) manual page. go weight some sequences. you got this. 💖🧚🦋🍓⭐

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