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Hmmer: Biological sequence analysis using profile hidden Markov models
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Some information about Hmmer from the Debian-Med project.
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Hmmer is a suite of programs which use profile hidden Markov models
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(profile HMMs) to model the primary structure consensus of a family of
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protein or nucleic acid sequences.
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Homepage: http://hmmer.wustl.edu/
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You can get a good overview by the main manpage:
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The Hmmer users guide is available at
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http://localhost/doc/hmmer/hmmer-html/index.html