## SYNOPSIS

**hmmcalibrate**

*[options]*

*hmmfile*

## DESCRIPTION

**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.

## 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
**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.

## 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/