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ProtPhylo is a web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. Prot-Phylo infers functional associations by comparing protein phylogenetic profiles (co-occurrence patterns of orthology relationships) for more than 9.7 million non-redundant protein sequences from all three domains of life. Users can query any of 2048 fully sequenced organisms, including 1678 bacteria, 255 eukaryotes and 115 archaea. Indoi:10.1093/nar/gkv455 pmid:25956654 pmcid:PMC4489284 fatcat:ifwzhjf5zrhshjiu34ar6x3txi