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) 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 Infernal web page ().

AUTHOR

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