hmmcalibrate - calibrate HMM search statistics
hmmcalibrate [options] hmmfile
hmmcalibrate 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 re-saves
hmmfile now including the EVD parameters.
hmmcalibrate may take several minutes (or longer) to run. While it is
running, a temporary file called hmmfile.xxx is generated in your
working directory. If you abort hmmcalibrate prematurely (ctrl-C, for
instance), your original hmmfile will be untouched, and you should
delete the hmmfile.xxx temporary file.
-h Print brief help; includes version number and summary of all
options, including expert options.
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).
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.
Save a histogram of the scores and the fitted theoretical curve
to file <f>.
Set the mean length of the synthetic sequences to <x>, where <x>
is a positive real number. The default is 350.
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. 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 hmmcalibrate-pvm must be installed
on all the PVM nodes. Optional PVM support must have been
compiled into HMMER.
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.
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 hmmcalibrate on the
same HMM will give slightly different results. You can use this
option to generate reproducible results for different
hmmcalibrate runs on the same HMM.
Master man page, with full list of and guide to the individual man
pages: see hmmer(1).
For complete documentation, see the user guide that came with the
distribution (Userguide.pdf); or see the HMMER web page,
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
HHMI/Dept. of Genetics
Washington Univ. School of Medicine
4566 Scott Ave.
St Louis, MO 63110 USA