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
Versions
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.
Access
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 opensource.org/licenses/BSD-3-Clause.
Usage
Usage on Owens
Set-up on Owens
HMMER usage is controlled via modules. To load the default version of HMMER module, usemodule 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, usemodule load hmmer.