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