HMMER
by Sean R. Eddy
1992
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Profile hidden Markov models (profile HMMs) can be used to do database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. User inputs a multiple sequence alignment; HMMER builds a statistical model called a "hidden Markov model" which the user can then use as a query into a sequence database to find (and/or align) additional homologues of the sequence family.