hmmpress - Man Page

prepare an HMM database for hmmscan


hmmpress [options] <hmmfile>


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 contains precomputed data structures for the fast heuristic filter (the MSV filter). The <hmmfile>.h3p file contains precomputed data structures for the rest of each profile.

<hmmfile> may not be '-' (dash); running hmmpress on a standard input stream rather than a file is not allowed.



Help; print a brief reminder of command line usage and all available options.


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 ().


Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA


February 2015 HMMER 3.1b2 HMMER Manual