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hmmpress(1) HMMER Manual hmmpress(1)


hmmpress - prepare a profile database for hmmscan


hmmpress [options] hmmfile


Constructs binary compressed datafiles for hmmscan, starting from a profile database hmmfile in standard HMMER3 format. 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 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 (


Copyright (C) 2020 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.

For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (

Nov 2020 HMMER 3.3.2