PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Huerta Cepas, Jaime; Capella Gutiérrez, Salvador Jesús, 1985-; Pryszcz, Leszek Piotr, 1985-; Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973-

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

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dc.contributor.author Huerta Cepas, Jaimeca
dc.contributor.author Capella Gutiérrez, Salvador Jesús, 1985-ca
dc.contributor.author Pryszcz, Leszek Piotr, 1985-ca
dc.contributor.author Marcet Houben, Marinaca
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
dc.date.accessioned 2014-05-14T07:34:20Z
dc.date.available 2014-05-14T07:34:20Z
dc.date.issued 2014ca
dc.description.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.
dc.description.sponsorship Spanish ministry of Economy and Competitiveness [BIO2012-37161]; a Grant from the Qatar National/nResearch Fund [NPRP 5-298-3-086]; a the European Research Council under the European Union’s Seventh/nFramework Programme [FP/2007-2013/ERC and ERC-/n2012-StG-310325]; Juan de La Cierva postdoctoral program (to J.H.C.) and La Caixa-CRG International Fellowship Program (to L.P.P.). Funding for open access charge: Internal budget from the CRG
dc.format.mimetype application/pdfca
dc.identifier.citation Huerta-Cepas J, Capella-Gutiérrez S, Pryszcz LP, Marcet-Houben M, Gabaldón T. PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res. 2014;42(1):D897-D902. DOI 10.1093/nar/gkt1177ca
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkt1177
dc.identifier.issn 0305-1048ca
dc.identifier.uri http://hdl.handle.net/10230/22485
dc.language.iso engca
dc.publisher Oxford University Pressca
dc.relation.ispartof Nucleic Acids Research. 2014;42(1):D897-D902
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/310325ca
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2012-37161
dc.rights.accessRights info:eu-repo/semantics/openAccessca
dc.rights.uri http://creativecommons.org/licenses/by/3.0/
dc.subject.other Filogènia
dc.subject.other Genètica
dc.subject.other Genòmica
dc.title PhylomeDB v4: zooming into the plurality of evolutionary histories of a genomeca
dc.type info:eu-repo/semantics/articleca
dc.type.version info:eu-repo/semantics/publishedVersionca

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