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/