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 often used together with a profile database, such as Pfam or many of the databases that participate inInterpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer.
HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST.
To see what versions of HMMER are available type
module avail hmmer
To see what other modules are needed, what commands are available and how to get additional help type
module help hmmer
To use HMMER, include a command like this in your batch script to load the HMMER module:
module load hmmer
Be sure you also load any other modules needed, as listed by the
module help hmmer command.