title: PhylomeDB: a database for genome-wide collections of gene phylogenies.
abstract: The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. To provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at http://phylomedb.bioinfo.cipf.es.
authors.affiliation: Bioinformatics Department, Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler, 13 Valencia 46013, Spain.
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.forename: Anibal
authors.initials: A
authors.lastname: Bueno
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
mesh_terms: D001483:Base Sequence; D004926:Escherichia coli / Q000145:classification / Q000235:genetics; D005796:Genes; D023281:Genomics; D049690:History, Ancient; D006801:Humans; D010802:Phylogeny; D011506:Proteins / Q000145:classification / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D011506:Proteins