hmm2calibrate(1)

💖 hmm2calibrate — calibrate HMM search statistics 💖

okay bestie, welcome to the manual page for hmm2calibrate, part of the HMMER Manual (HMMER 2.3.2, no cap). she's a little diva, she takes her time, but she makes your HMM stats actually trustworthy. let's get into it 🫶

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✨ NAME ✨

hmm2calibrate — calibrate HMM search statistics 💅

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🌸 SYNOPSIS 🌸

hmm2calibrate [options] hmmfile

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🦋 DESCRIPTION 🦋

so here's the tea, bestie: hmm2calibrate reads an HMM file from hmmfile, scores a large number of synthesized random sequences with it, fits an extreme value distribution (EVD) to the histogram of those scores, and then re-saves hmmfile — except now it's got the EVD parameters baked in. iconic. ✨

heads up though: hmm2calibrate may take several minutes (or longer) to run. she is not a quick lil errand, she is a whole journey. 😭

while she's running, a temporary file called hmmfile.xxx gets generated in your working directory. and if you abort hmm2calibrate prematurely (ctrl-C, for instance), your original hmmfile will be untouched — slay — and you should delete the hmmfile.xxx temporary file. don't just leave it there being messy. 🙈

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🎀 OPTIONS 🎀

• -h — print brief help; includes the version number and a summary of all options, including the expert options. the lil cheat sheet, we love her. 💖

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👑 EXPERT OPTIONS 👑

💜 --cpu <n>

sets the maximum number of CPUs that the program will run on. the default is to use all CPUs in the machine. this overrides the HMMER_NCPU environment variable. ngl, this only affects threaded versions of HMMER (which is the default on most systems).

💜 --fixed <n>

fix the length of the random sequences to <n>, where <n> is a positive (and reasonably sized) integer. the default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution. mix it up, periodt.

💜 --histfile <f>

save a histogram of the scores and the fitted theoretical curve to file <f>. cute lil receipt of what went down. 🍓

💜 --mean <x>

set the mean length of the synthetic sequences to <x>, where <x> is a positive real number. the default is 350.

💜 --num <n>

set the number of synthetic sequences to <n>, where <n> is a positive integer. if <n> is less than about 1000, the fit to the EVD may fail — so like, be careful, bestie. 💀 higher numbers of <n> will give better determined EVD parameters. the default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time.

💜 --pvm

run on a Parallel Virtual Machine (PVM). the PVM must already be running. the client program hmm2calibrate-pvm must be installed on all the PVM nodes. optional PVM support must have been compiled into HMMER. it's giving distributed computing, it's giving extra setup, iykyk. 🔥

💜 --sd <x>

set the standard deviation of the synthetic sequence length distribution to <x>, where <x> is a positive real number. the default is 350. note that the Gaussian is left-truncated so that no sequences have lengths <= 0. no zero-length nonsense allowed on this account. 🧚

💜 --seed <n>

set the random seed to <n>, where <n> is a positive integer. the default is to use time() to generate a different seed for each run, which means that two different runs of hmm2calibrate on the same HMM will give slightly different results. you can use this option to generate reproducible results for different hmm2calibrate runs on the same HMM. ✨

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🌈 SEE ALSO 🌈

master man page, with full list of and guide to the individual man pages: see hmmer2(1). 👑

for complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, http://hmmer.janelia.org/.

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💖 COPYRIGHT 💖

Copyright (C) 1992-2003 HHMI/Washington University School of Medicine. Freely distributed under the GNU General Public License (GPL). See the file COPYING in your distribution for details on redistribution conditions.

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🫶 AUTHOR 🫶

Sean Eddy HHMI/Dept. of Genetics Washington Univ. School of Medicine 4566 Scott Ave. St Louis, MO 63110 USA http://www.genetics.wustl.edu/eddy/

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and that's the whole page, bestie — HMMER 2.3.2, dated Oct 2003, written by the one and only Sean Eddy. go calibrate something gorgeous. 💅✨