HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMS). HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models.

Availability and Restrictions


HMMER is available on the OSC clusters. These are the versions currently available:

Version Owens Pitzer Notes
3.3.2 X X  


You can use module spider hmmer to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


HMMER is available to all OSC users.

Publisher/Vendor/Repository and License Type

Copyright (C) 2020 Howard Hughes Medical Institute.

HMMER and its documentation are feely distributed under the 3-Clause BSD open source license. For a copy of the license, see


Usage on Owens

Set-up on Owens

HMMER usage is controlled via modules. To load the default version of HMMER module, use module load hmmer. To select a particular software version, use module load hmmer/version. For example, use module load hmmer/3.3.2 to load HMMER version 3.3.2 on Owens.

Usage on Pitzer

Set-up on Pitzer

HMMER usage is controlled via modules. Load one of the HMMER module files at the command line, in your shell initialization script, or in your batch scripts. To load the default version of HMMER module, use module load hmmer.

Further Reading

Fields of Science: