profile hidden Markov models for protein sequence analysis

 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.