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


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


       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.


       --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

              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.)


       For complete documentation, see the User’s Guide  (Userguide.pdf)  that
       came   with   the   distribution;   or   see  the  Infernal  web  page,


       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.


       Eric Nawrocki, Diana Kolbe, and Sean Eddy
       HHMI Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147