Provided by: hmmer2_2.3.2-7ubuntu1_amd64 bug

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/