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.TH "hmm2calibrate" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
.SH NAME
.TP
hmm2calibrate - calibrate HMM search statistics
.SH SYNOPSIS
.B hmm2calibrate
.I [options]
.I hmmfile
.SH DESCRIPTION
.B hmm2calibrate
reads an HMM file from
.I hmmfile,
scores a large number of synthesized random sequences with it, fits an
extreme value distribution (EVD) to the histogram of those scores, and
re-saves
.I hmmfile
now including the EVD parameters.
.PP
.B hmm2calibrate
may take several minutes (or longer) to run.
While it is running, a temporary file called
.I hmmfile.xxx
is generated in your working directory.
If you abort
.B hmm2calibrate
prematurely (ctrl-C, for instance), your original
.I hmmfile
will be untouched, and you should delete the
.I hmmfile.xxx
temporary file.
.SH OPTIONS
.TP
.B -h
Print brief help; includes version number and summary of
all options, including expert options.
.SH EXPERT OPTIONS
.TP
.BI --cpu " <n>"
Sets the maximum number of CPUs that the program
will run on. The default is to use all CPUs
in the machine. Overrides the HMMER_NCPU
environment variable. Only affects threaded
versions of HMMER (the default on most systems).
.TP
.BI --fixed " <n>"
Fix the length of the random sequences to
.I <n>,
where
.I <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.
.TP
.BI --histfile " <f>"
Save a histogram of the scores and the fitted theoretical curve
to file
.I <f>.
.TP
.BI --mean " <x>"
Set the mean length of the synthetic sequences to
.I <x>,
where
.I <x>
is a positive real number. The default is 350.
.TP
.BI --num " <n>"
Set the number of synthetic sequences to
.I <n>,
where
.I <n>
is a positive integer. If
.I <n> is less than about 1000, the fit to the EVD may fail.
Higher numbers of
.I <n>
will give better determined EVD parameters. The default
is 5000; it was empirically chosen as
a tradeoff between accuracy and computation time.
.TP
.B --pvm
Run on a Parallel Virtual Machine (PVM). The PVM must
already be running. The client program
.B hmm2calibrate-pvm
must be installed on all the PVM nodes.
Optional PVM support must have been compiled into
HMMER.
.TP
.BI --sd " <x>"
Set the standard deviation of the synthetic sequence
length distribution to
.I <x>,
where
.I <x>
is a positive real number. The default is 350. Note that the
Gaussian is left-truncated so that no sequences have lengths
<= 0.
.TP
.BI --seed " <n>"
Set the random seed to
.I <n>,
where
.I <n>
is a positive integer. The default is to use
.B time()
to generate a different seed for each run, which
means that two different runs of
.B hmm2calibrate
on the same HMM will give slightly different
results. You can use
this option to generate reproducible results for
different
.B hmm2calibrate
runs on the same HMM.
.SH SEE ALSO
Master man page, with full list of and guide to the individual man
pages: see
.B hmmer2(1).
.PP
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/.
.SH COPYRIGHT
.nf
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
Freely distributed under the GNU General Public License (GPL).
.fi
See the file COPYING in your distribution for details on redistribution
conditions.
.SH AUTHOR
.nf
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/
.fi
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