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 format.  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 Infernal distribution
       (Userguide.pdf); or see the Infernal web page ().

COPYRIGHT

       Copyright (C) 2013 Howard Hughes Medical Institute.
       Freely distributed under the GNU General Public License (GPLv3).

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

AUTHOR

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