hmmstat(1)

📦
version 3.4 · 2 versions
, in debian trixie, nixos 26.05, nixpkgs unstable, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 hmmstat(1) — bestie edition 💖

okay so this is hmmstat, straight outta the HMMER Manual (we're on HMMER 3.4, for the record, and I will absolutely be yapping about that at the end 🫶).

✨ NAME ✨

hmmstat — summary statistics for a profile file. that's it, that's the girl. she reads your profiles and gives you the numbers 💅

✨ SYNOPSIS ✨

hmmstat [options] hmmfile

✨ DESCRIPTION ✨

The hmmstat utility prints out a tabular file of summary statistics for each profile in hmmfile.

hmmfile may be '-' (a dash character), in which case profiles are read from a stdin pipe instead of from a file. iconic behavior honestly

The columns are:

  • idx — The index of this profile, numbering each profile in the file starting from 1.
  • name — The name of the profile.
  • accession — The optional accession of the profile, or "-" if there is none. (yes, a literal dash. she said "no thanks" 🎀)
  • nseq — The number of sequences that the profile was estimated from.
  • eff_nseq — The effective number of sequences that the profile was estimated from, after HMMER applied an effective sequence number calculation such as the default entropy weighting.
  • M — The length of the model in consensus residues (match states).
  • relent — Mean relative entropy per match state, in bits. This is the expected (mean) score per consensus position. This is what the default entropy-weighting method for effective sequence number estimation focuses on, so for default HMMER3 models, you expect this value to reflect the default target for entropy-weighting.
  • info — Mean information content per match state, in bits. Probably not useful. Information content is a slightly different calculation than relative entropy. (she's giving "we keep her around for historical reasons" energy ngl)
  • p relE — Mean positional relative entropy, in bits. This is a fancier version of the per-match-state relative entropy, taking into account the transition (insertion/deletion) probabilities; it may be a more accurate estimation of the average score contributed per model consensus position. fancier version? we love an upgrade arc ✨
  • compKL — Kullback-Leibler divergence from the default background frequency distribution to the average composition of the profile's consensus match states, in bits. The higher this number, the more biased the residue composition of the profile is. Highly biased profiles can slow the HMMER3 acceleration pipeline, by causing too many nonhomologous sequences to pass the filters.
heads up bestie: that compKL thing is not just a cute number. high bias = the HMMER3 acceleration pipeline gets slowed down because too many nonhomologous sequences make it through the filters. so a spicy compKL is lowkey a performance warning 😭

✨ OPTIONS ✨

  • -h — Help; print a brief reminder of command line usage and all available options.

✨ SEE ALSO ✨

See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.

For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (http://hmmer.org/).

Copyright (C) 2023 Howard Hughes Medical Institute. Freely distributed under the BSD open source license.

For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (http://hmmer.org/).

✨ AUTHOR ✨

http://eddylab.org

and that's the whole page, bestie 💜 this was HMMER 3.4, dated Aug 2023, and yeah it really did end with hmmstat(1) like a little bow on top 🎀 go forth and stat your hmms 👑

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