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HMMER is an implementation of profile HMM methods for sensitive database
searches using multiple sequence alignments as queries.
Basically, you give HMMER a multiple sequence alignment as input; it builds
a statistical model called a "hidden Markov model" which you can then use as
a query into a sequence database to find (and/or align) additional
homologues of the sequence family.
WWW: http://hmmer.wustl.edu/
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