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NAME

       cm2hmm - build a rigorous HMM-based filter from an existing covariance model (CM)

SYNOPSIS

       cm2hmm  cmfile  hmmfile  background  [background  parameters] HMMtype optimizer [optimizer
       parameters]

DESCRIPTION

       cm2hmm reads a covariance model (CM) from cmfile, constructs a hidden-Markov  model  (HMM)
       that  preserves  some  information of the CM and saves the HMM to hmmfile.  The HMM can be
       used as a rigorous pre-filtering step to searching with the CM.

       The CM file must be in the standard format output used by Infernal.

OPTIONS

       --help Print brief help; includes summary of command-line parameters.

       background [background parameters]
              Select the model of background sequence.  uniform gives all bases equal probability
              (25%).   gc  <fraction>  specifies  the G+C content.  <fraction> should be a number
              between 0 and 1.  file <filename> loads the base distribution  from  a  file  in  a
              specific format.

       HMMtype
              Specify the type of HMM to be used; options are compact and expanded.  Compact-type
              models are generally faster, but expanded-type models may provide better filtering.

       optimizer [optimizer parameters]
              Specify which mathematical optimizer is to be  used  to  create  the  final  model.
              Currently  the  only  option is cfsqp which takes two paramters: <B> <C>.  B=0, C=1
              are reasonable choices.  (See the CFSQP manual for further details.)

SEE ALSO

       For complete documentation, see the  User's  Guide  (Userguide.pdf)  that  came  with  the
       distribution; or see the Infernal web page, http://infernal.janelia.org/.

COPYRIGHT

       Copyright (C) 2009 HHMI Janelia Farm Research Campus.
       Freely distributed under the GNU General Public License (GPLv3).
       See the file COPYING that came with the source for details on redistribution conditions.

AUTHOR

       Eric Nawrocki, Diana Kolbe, and Sean Eddy
       HHMI Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147
       http://selab.janelia.org/