title: EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
abstract: We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic approach. All data are made available in a number of formats and will be kept up to date with the Ensembl project.
authors.affiliation: EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
authors.forename: Albert J
authors.initials: AJ
authors.lastname: Vilella
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Abel
authors.initials: A
authors.lastname: Ureta-Vidal
authors.forename: Li
authors.initials: L
authors.lastname: Heng
authors.forename: Richard
authors.initials: R
authors.lastname: Durbin
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D020440:Gene Duplication; D006801:Humans; D008954:Models, Biological; D005810:Multigene Family; D010802:Phylogeny; D017385:Sequence Homology; D012984:Software; D026801:Synteny; D014714:Vertebrates / Q000145:classification* / Q000235:genetics