hmmpress(1) [debian man page]
hmmpress(1) HMMER Manual hmmpress(1) NAME
hmmpress - prepare an HMM database for hmmscan SYNOPSIS
hmmpress [options] <hmmfile> DESCRIPTION
Starting from a profile database <hmmfile> in standard HMMER3 format, construct binary compressed datafiles for hmmscan. The hmmpress step is required for hmmscan to work. Four files are created: <hmmfile>.h3m, <hmmfile>.h3i, <hmmfile>.h3f, and <hmmfile>.h3p. The <hmmfile>.h3m file contains the profile HMMs and their annotation in a binary format. The <hmmfile>.h3i file is an SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file con- tains precomputed data structures for the fast heuristic filter (the MSV filter). The <hmmfile>.h3p file contains precomputed data struc- tures for the rest of each profile. OPTIONS
-h Help; print a brief reminder of command line usage and all available options. -f Force; overwrites any previous hmmpress'ed datafiles. The default is to bitch about any existing files and ask you to delete them first. SEE ALSO
See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package. For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@). COPYRIGHT
@HMMER_COPYRIGHT@ @HMMER_LICENSE@ For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@). AUTHOR
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmpress(1)
Check Out this Related Man Page
hmmconvert(1) HMMER Manual hmmconvert(1) NAME
hmmconvert - convert profile file to a HMMER format SYNOPSIS
hmmconvert [options] <hmmfile> DESCRIPTION
The hmmconvert utility converts an input profile file to different HMMER formats. By default, the input profile can be in any HMMER format, including old/obsolete formats from HMMER2, ASCII or binary; the output profile is a current HMMER3 ASCII format. OPTIONS
-h Help; print a brief reminder of command line usage and all available options. -a Output profiles in ASCII text format. This is the default. -b Output profiles in binary format. -2 Output in legacy HMMER2 ASCII text format, in ls (glocal) mode. This allows HMMER3 models to be converted back to a close approxima- tion of HMMER2, for comparative studies. --outfmt <s> Output in a HMMER3 ASCII text format other then the most current one. Valid choices for <s> are 3/b or 3/a. The current format is 3/b, and this is the default. There is a slightly different format 3/a that was used in some alpha test code. SEE ALSO
See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package. For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@). COPYRIGHT
@HMMER_COPYRIGHT@ p@HMMER_LICENSE@ For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@). AUTHOR
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org " HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmconvert(1)