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SCI-PHY

Subfamily Classification In PHYlogenomics.  Given a multiple sequence alignment, uses a minimum-encoding-cost criterion to create subfamilies intended to represent proteins with close evolutionary and functional relationships.  Outputs include subfamily definitions and hidden Markov models (HMMs) in both HMMER and UCSC SAM formats.  More information.
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References to the SCI-PHY algorithm or software should cite this paper: Brown DP, Krishnamurthy N, Sjölander K, "Automated Protein Subfamily Identification and Classification," PLoS Computational Biology 2007, 3(8): e160 doi:10.1371/journal.pcbi.0030160.  PDF.  Supplementary Data.

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