.TH "hmmconvert" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual" .SH NAME .TP hmmconvert - convert between profile HMM file formats .SH SYNOPSIS .B hmmconvert .I [options] .I oldhmmfile .I newhmmfile .SH DESCRIPTION .B hmmconvert reads an HMM file from .I oldhmmfile in any HMMER format, and writes it to a new file .I newhmmfile in a new format. .I oldhmmfile and .I 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 .I (-b) GCG profile .I (-p) , and Compugen XSW extended profile .I (-P). .SH OPTIONS .TP .B -a Convert to HMMER 2 ASCII file. This is the default, so this option is unnecessary. .TP .B -b Convert to HMMER 2 binary file. .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .TP .B -p Convert to GCG profile .prf format. .TP .B -A Append mode; append to .I newhmmfile rather than creating a new file. .TP .B -F Force; if .I newhmmfile already exists, and .I -A is not being used to append to the file, hmmconvert will refuse to clobber the existing file unless .I -F is used. .TP .B -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.) .SH SEE ALSO Master man page, with full list of and guide to the individual man pages: see .B hmmer(1). .PP For complete documentation, see the user guide that came with the distribution (Userguide.pdf); or see the HMMER web page, http://hmmer.wustl.edu/. .SH COPYRIGHT .nf Copyright (C) 1992-2003 HHMI/Washington University School of Medicine. Freely distributed under the GNU General Public License (GPL). .fi See the file COPYING in your distribution for details on redistribution conditions. .SH AUTHOR .nf 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/ .fi
