Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
cmpress(1)			Infernal Manual			    cmpress(1)

NAME
       cmpress - prepare a covariance model database for cmscan

SYNOPSIS
       cmpress [options] _cmfile_

DESCRIPTION
       Starting	 from  a CM database _cmfile_ in standard Infernal-1.1 format,
       construct binary	compressed datafiles for cmscan.  The cmpress step  is
       required	for cmscan to work.

       The  _cmfile_ must be have already been calibrated with cmcalibrate for
       cmpress to work.

       Four files are created: _cmfile_.i1m, _cmfile_.i1i,  _cmfile_.i1f,  and
       _cmfile_.i1p.   The  _cmfile_.i1m  file contains	the covariance models,
       associated filter p7 profile HMMs and their annotation in a binary for-
       mat.   The _cmfile_.i1i file is an SSI index for	the _cmfile_.i1m file.
       The _cmfile_.i1f	file contains precomputed data structures for the fast
       heuristic  filter  (the	SSV  filter) for the filter p7 profile HMMs in
       _cmfile_.  The _cmfile_.i1p file	contains precomputed  data  structures
       for the rest of each profile filter p7 HMM.

       _cmfile_	 may  not  be  '-' (dash); running cmpress on a	standard input
       stream rather than a file is not	allowed.

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

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

SEE ALSO
       See infernal(1) for a master man	page with a list of all	the individual
       man pages for programs in the Infernal package.

       For complete documentation, see the user	guide that came	with your  In-
       fernal distribution (Userguide.pdf); or see the Infernal	web page ().

COPYRIGHT
       Copyright (C) 2019 Howard Hughes	Medical	Institute.
       Freely distributed under	the BSD	open source license.

       For  additional	information  on	 copyright and licensing, see the file
       called COPYRIGHT	in your	Infernal source	distribution, or see  the  In-
       fernal web page ().

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

Infernal 1.1.3			   Nov 2019			    cmpress(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT | AUTHOR

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=cmpress&sektion=1&manpath=FreeBSD+12.2-RELEASE+and+Ports>

home | help