BPG home  |  BPG resources  |  New SCI-PHY run  |  Help

 

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.
Paste alignment in aligned FASTA format or A2M format:
How to define your own subfamilies
OR
Upload FASTA or A2M file:
 
Send email to:
Subject line:
   


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.
Email questions or comments to phylo.