title: PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.
abstract: Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88. 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.forename: Salvador
authors.initials: S
authors.lastname: Capella-Gutiérrez
authors.forename: Leszek P
authors.initials: LP
authors.lastname: Pryszcz
authors.forename: Marina
authors.initials: M
authors.lastname: Marcet-Houben
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D020407:Internet; D010802:Phylogeny; D011506:Proteins / Q000145:classification / Q000235:genetics; D020543:Proteome
chemical_list: D011506:Proteins; D020543:Proteome