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 (http://eddylab.org/infernal/).

COPYRIGHT

       Copyright (C) 2023 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 Infernal web page (http://eddylab.org/infernal/).

AUTHOR

       http://eddylab.org

Infernal 1.1.5                                      Sep 2023                                          cmpress(1)