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       hmmconvert - convert between profile HMM file formats


       hmmconvert [options] oldhmmfile newhmmfile


       hmmconvert  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

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


       -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

       -F     Force; if newhmmfile already exists, and -A is not being used to
              append to the  file,  hmmconvert  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.)


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

       For complete documentation, see the  user  guide  that  came  with  the
       distribution    (Userguide.pdf);   or   see   the   HMMER   web   page,


       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


       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA