HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries.
The version of HMMER that is distributed with this version of Rocks was obtained from here. The version as of code freeze is v2.3.2 and is distributed by WU, St.Louis under the GNU General Public License v2.0.
HMMER is setup in the /opt/Bio/hmmer directory. The HMMER execution environment is setup automatically by the login scripts. The environment contains HMMER_DB variable which points to the directory containing the hmmer databases. By default, this is set to /share/bio/hmmer/db/.
HMMER has many modes of execution. Please run
$ man hmmer
You may also refer to the Users Guide present here. This guide is also available on your rocks installation at /opt/Bio/hmmer/Userguide.pdf
There is also a tutorial available on your cluster at /opt/Bio/hmmer/tutorial/ . The description of how to use the tutorial is given in the Userguide.pdf file.