SYNOPSIShmmcalibrate [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.
Print brief help; includes version number and summary of
all options, including 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. Overrides the HMMER_NCPU
environment variable. Only affects threaded
versions of HMMER (the default on most systems).
- --fixed <n>
Fix the length of the random sequences to
is a positive (and reasonably sized) integer.
The default is instead to generate sequences with
a variety of different lengths, controlled by a Gaussian
- --histfile <f>
Save a histogram of the scores and the fitted theoretical curve
- --mean <x>
Set the mean length of the synthetic sequences to
is a positive real number. The default is 350.
- --num <n>
Set the number of synthetic sequences to
is a positive integer. If
<n> is less than about 1000, the fit to the EVD may fail.
Higher numbers of
will give better determined EVD parameters. The default
is 5000; it was empirically chosen as
a tradeoff between accuracy and computation time.
Run on a Parallel Virtual Machine (PVM). The PVM must
already be running. The client program
must be installed on all the PVM nodes.
Optional PVM support must have been compiled into
- --sd <x>
Set the standard deviation of the synthetic sequence
length distribution to
is a positive real number. The default is 350. Note that the
Gaussian is left-truncated so that no sequences have lengths
- --seed <n>
Set the random seed to
is a positive integer. The default is to use
to generate a different seed for each run, which
means that two different runs of
on the same HMM will give slightly different
results. You can use
this option to generate reproducible results for
runs on the same HMM.
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.
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/