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cm2hmm(1) [debian man page]

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)

Check Out this Related Man Page

hmmpress(1)							   HMMER Manual 						       hmmpress(1)

NAME

       hmmpress - prepare an HMM database for hmmscan

SYNOPSIS

       hmmpress [options] <hmmfile>

DESCRIPTION

       Starting from a profile database <hmmfile> in standard HMMER3 format, construct binary compressed datafiles for hmmscan.  The hmmpress step
       is required for hmmscan to work.

       Four files are created: <hmmfile>.h3m, <hmmfile>.h3i, <hmmfile>.h3f, and <hmmfile>.h3p.	The <hmmfile>.h3m file contains the  profile  HMMs
       and  their  annotation in a binary format.  The <hmmfile>.h3i file is an SSI index for the <hmmfile>.h3m file.  The <hmmfile>.h3f file con-
       tains precomputed data structures for the fast heuristic filter (the MSV filter).  The <hmmfile>.h3p file contains precomputed data  struc-
       tures for the rest of each profile.

OPTIONS

       -h     Help; print a brief reminder of command line usage and all available options.

       -f     Force;  overwrites  any  previous hmmpress'ed datafiles. The default is to bitch about any existing files and ask you to delete them
	      first.

SEE ALSO

       See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.

       For complete documentation, see the user guide that came  with  your  HMMER  distribution  (Userguide.pdf);  or	see  the  HMMER  web  page
       (@HMMER_URL@).

COPYRIGHT

       @HMMER_COPYRIGHT@
       @HMMER_LICENSE@

       For  additional	information  on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER
       web page (@HMMER_URL@).

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

HMMER 
@HMMER_VERSION@						   @HMMER_DATE@ 						       hmmpress(1)
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