title: Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.
abstract: Phylogenomic analysis addresses the limitations of function prediction based on annotation transfer, and has been shown to enable the highest accuracy in prediction of protein molecular function. The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction and SCI-PHY subfamily identification. The PhyloBuilder web server provides an integrated phylogenomic pipeline starting with a user-supplied protein sequence, proceeding to homolog identification, multiple alignment, phylogenetic tree construction, subfamily identification and structure prediction. The Berkeley Phylogenomics Group resources are available at http://phylogenomics.berkeley.edu.
authors.affiliation: Berkeley Phylogenomics Group, University of California, Berkeley, USA.
authors.forename: Jake Gunn
authors.initials: JG
authors.lastname: Glanville
authors.forename: Dan
authors.initials: D
authors.lastname: Kirshner
authors.forename: Nandini
authors.initials: N
authors.lastname: Krishnamurthy
authors.forename: Kimmen
authors.initials: K
authors.lastname: Sjölander
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D030541:Databases, Genetic; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008957:Models, Genetic; D010802:Phylogeny; D011487:Protein Conformation; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface