NAME

       cmconvert - convert Infernal covariance model files

SYNOPSIS

       cmconvert [options] <cmfile>

DESCRIPTION

       The  cmconvert  utility  converts  an  input  covariance  model file to different Infernal
       formats.

       By default, the input CM file can be any CM file created by Infernal version 1.0 or later;
       the  output  CM  file is a current Infernal format. Files from versions older than version
       1.0 cannot be converted.

       <cmfile> may be '-' (dash), which means reading this input from stdin rather than a file.

OPTIONS

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

       -a     Output profiles in ASCII text format. This is the default.

       -b     Output profiles in binary format.

       -1     Output in legacy Infernal1 (Infernal v1.0 through v1.0.2) ASCII text format. Due to
              important changes between version v1.0.2 and v1.1, any E-value statistic parameters
              calculated by cmcalibrate in <cmfile> will not be written to the  converted  output
              file.

       --mlhmm
              Do  not  output a CM file. Instead, output one maximum likelihood p7 HMM built from
              each CM in <cmfile> in HMMER3 ASCII text format. The HMM will have been constructed
              to  be as similar as possible to the CM, without modeling secondary structure. This
              option could be useful for comparative studies of Infernal and HMMER3.

       --fhmm Do not output a CM file. Instead, output the filter p7 HMM for each CM in  <cmfile>
              in HMMER3 ASCII text format.

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