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ICHEC Software

Information about software packages installed on the ICHEC systems.


Versions Installed

Stokes: 3.0

Stoney: 3.0


HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called “profile hidden Markov models” (profile HMMs).

Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.


HMMER is licensed under the GPLv3 (GNU General Public License, version 3).



Additional Notes

To use HMMER load the relevant environment module:

module load hmmer

The HMMER package consists of serial programs which may be used in conjunction with the taskfarm utility for batch jobs. Further information can be obtained at http://hmmer.janelia.org/.

How to cite HMMER:

Durbin R., Eddy S., Krogh A. and Mitchison G. (1998)
Biological sequence analysis: probabilistic models of proteins and nucleic acids
Cambridge University Press.

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