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       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  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 temporary file.


       -h     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 <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 hmmcalibrate-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 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


       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA