cmstat(1)

okay bestie so this is the manual page for cmstat(1), straight out of the Infernal Manual 💅 it's a whole mood and also extremely useful, so let's get into it 🫶

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✨ NAME ✨

cmstat — summary statistics for a covariance model file 🎀

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🌸 SYNOPSIS 🌸

cmstat [options] <cmfile>

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🦋 DESCRIPTION 🦋

so what does cmstat actually do? it prints out a tabular file of summary statistics for every single covariance model chilling inside <cmfile> ✨ one line per model, no cap.

and here's a cute little trick: <cmfile> can be - (yes, literally just a dash character), and if you do that, the CMs get read from a <stdin> pipe instead of from an actual file 🍓 iconic behavior honestly.

by default, cmstat prints general statistics about the model and the alignment it was built from, one line per model, in a tabular format. the columns are:

• idx — the index of this profile, numbering each one in the file starting from 1.
• name — the name of the profile.
• accession — the optional accession of the profile, or - if there isn't one. (not me being optional 💀)
• 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 Infernal applied an effective sequence number calculation, like the default entropy weighting ✨
• clen — the length of the model in consensus residues (a.k.a. match states).
• W — the expected maximum length of a hit to the model.
• bps — the number of basepairs in the model.
• bifs — the number of bifurcations in the model.
• model — what type of model will be used by default in cmsearch and cmscan for this profile, either "cm" or "hmm". for profiles with 0 basepairs, this will be "hmm" (unless the --nohmmonly option is used, bestie). for all other profiles, this will be "cm".
• rel entropy, cm: — mean relative entropy per match state, in bits. this is the expected (mean) score per consensus position 👑 and it's literally what the default entropy-weighting method for effective sequence number estimation focuses on, so for default Infernal, this value will often reflect the default target for entropy-weighting. but if the "model" field for this profile is "hmm", this field will be "-".
• rel entropy, hmm: — mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). the larger the difference between the CM and HMM relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs. it's giving structural girlie vs sequence girlie 🌈

now, if the model(s) in <cmfile> have been calibrated with cmcalibrate, the -E, -T, and -Z <n> options can be used to invoke an alternative output mode, reporting E-values and corresponding bit scores for a specified database size of <n> megabases (Mb) ✨

and if the model(s) have been calibrated and include Rfam GA, TC, and/or NC bit score thresholds, then the --cut_ga, --cut_tc, and/or --cut_nc options can be used to display E-values that correspond to those bit score thresholds 💖

separate bit scores or E-values will be displayed for each of the four possible CM search algorithm and model configuration pairs: local Inside, local CYK, glocal Inside and glocal CYK. periodt.

for profiles with zero basepairs (those with "hmm" in the "model" field), any E-value and bit score statistics will pertain to the profile HMM filter, instead of to the CM. this is also true for all profiles if the --hmmonly option is used 👀

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💅 OPTIONS 💅

• -h — help; print a brief reminder of command line usage and all available options 🙈
• -E <x1> — report bit scores that correspond to an E-value of <x1> in a database of <x> megabases (Mb), where <x> is 10 by default but settable with the -Z <x> option.
• -T <x1> — report E-values that correspond to a bit score of <x1> in a database of <x> megabases (Mb), where <x> is 10 by default but settable with the -Z <x> option.
• -Z <x> — with the -E, -T, --cut_ga, --cut_nc, and --cut_tc options, calculate E-values as if the target database size was <x> megabases (Mb). by default, <x> is 10.
• --cut_ga — report E-values that correspond to the GA (Rfam gathering threshold) bit score in a database of <x> megabases (Mb), where <x> is 10 by default but settable with the -Z <x> option.
• --cut_tc — report E-values that correspond to the TC (Rfam trusted cutoff) bit score in a database of <x> megabases (Mb), where <x> is 10 by default but settable with the -Z <x> option.
• --cut_nc — report E-values that correspond to the NC (Rfam noise cutoff) bit score in a database of <x> megabases (Mb), where <x> is 10 by default but settable with the -Z <x> option.
• --key <s> — only print statistics for CM with name or accession <s>, skip all other models in <cmfile>. very "just my fave, everyone else go home" energy 🎀
• --hmmonly — print statistics on the profile HMM filters for all profiles, instead of the CMs. this can be useful if you plan to use the --hmmonly option to cmsearch or cmscan 👑
• --nohmmonly — always print statistics on the CM for each profile, even for those with zero basepairs 💪

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🫶 SEE ALSO 🫶

• see infernal(1) for a master man page with a list of all the individual man pages for programs in the Infernal package ✨
• for complete documentation, see the user guide that came with your Infernal distribution (Userguide.pdf); or see the Infernal web page (http://eddylab.org/infernal/) 🌸

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🌈 COPYRIGHT 🌈

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 Infernal source distribution, or see the Infernal web page (http://eddylab.org/infernal/) 💜

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⭐ AUTHOR ⭐

http://eddylab.org 🦋

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and that's the whole page bestie 💖 this was Infernal 1.1.5, dated Sep 2023 — go forth and summarize those covariance models, you absolute icon 👑✨