NAME

       hmm2convert - convert between profile HMM file formats

SYNOPSIS

       hmm2convert [options] oldhmmfile newhmmfile

DESCRIPTION

       hmm2convert  reads an HMM file from oldhmmfile in any HMMER format, and writes it to a new
       file newhmmfile in a new format.  oldhmmfile and newhmmfile must be different  files;  you
       can't reliably overwrite the old file.  By default, the new HMM file is written in HMMER 2
       ASCII format.

       Available formats are HMMER 2 ASCII (default), HMMER 2 binary (-b) GCG profile (-p) ,  and
       Compugen XSW extended profile (-P).

OPTIONS

       -a     Convert to HMMER 2 ASCII file. This is the default, so this option is unnecessary.

       -b     Convert to HMMER 2 binary file.

       -h     Print  brief  help;  includes  version number and summary of all options, including
              expert options.

       -p     Convert to GCG profile .prf format.

       -A     Append mode; append to newhmmfile rather than creating a new file.

       -F     Force; if newhmmfile already exists, and -A is not being  used  to  append  to  the
              file, hmm2convert will refuse to clobber the existing file unless -F is used.

       -P     Convert  the  HMM  to Compugen XSW extended profile format, which is similar to GCG
              profile format but has two extra columns for delete-open and  delete-extend  costs.
              (I  do  not  believe  that  Compugen  publicly  supports  this  format;  it  may be
              undocumented.)

SEE ALSO

       Master man page, with full list of and guide to the individual man pages: see hmmer2(1).

       For        complete        documentation,        see        the         user         guide
       (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf);  or  see  the  HMMER web
       page, http://hmmer.janelia.org/.

COPYRIGHT

       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
       Freely distributed under the GNU General Public License (GPL).
       See the file COPYING in your distribution for details on redistribution conditions.

AUTHOR

       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA
       http://www.genetics.wustl.edu/eddy/