Hmmer: Biological sequence analysis using profile hidden Markov models 

Some information about Hmmer from the Debian Med project.

 Hmmer is a suite of programs which use profile hidden Markov models
 (profile HMMs) to model the primary structure consensus of a family of
 protein or nucleic acid sequences.

Homepage:  http://hmmer.wustl.edu/

You can get a good overview by the main manpage:

       man hmmer

The Hmmer users guide is available at

       http://localhost/doc/hmmer/hmmer-html/index.html
