debian man page for cm2hmm

cm2hmm(1)							  Infernal Manual							 cm2hmm(1)

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/

Infernal 1.0.2							   October 2009 							 cm2hmm(1)