NAME

       hmm2calibrate - calibrate HMM search statistics

SYNOPSIS

       hmm2calibrate [options] hmmfile

DESCRIPTION

       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 re-saves hmmfile now including the EVD parameters.

       hmm2calibrate  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
       hmm2calibrate prematurely (ctrl-C, for instance), your original hmmfile will be untouched,
       and you should delete the hmmfile.xxx temporary file.

OPTIONS

       -h     Print brief help; includes version number and summary  of  all  options,  including
              expert options.

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  <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.

       --histfile <f>
              Save a histogram of the scores and the fitted theoretical curve to file <f>.

       --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.  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.

       --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.

       --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.

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/.

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.

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/