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/

HMMER 2.3.2                                         Oct 2003                                    hmm2calibrate(1)