HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
alignments as queries.

Given a multiple sequence alignment as input, HMMER builds a statistical
model called a "hidden Markov model" which can then be used as a query into
a sequence database to find (and/or align) additional homologues of the
sequence family.

WWW: http://hmmer.janelia.org/