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/