{"doi":"10.1101/gr.073585.107","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.","journal":"Genome Research","year":2008,"id":8935,"datarank":18.3008410684546,"base_score":7.177782416195197,"endowment":7.177782416195197,"self_citation_contribution":1.0766673624292797,"citation_network_contribution":17.22417370602532,"self_endowment_contribution":1.0766673624292797,"citer_contribution":17.22417370602532,"corpus_percentile":92.18877135882832,"corpus_rank":97,"citation_count":1330,"citer_count":191,"citers_with_citation_signal":191,"citers_with_endowment":191,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8963,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2008-11-24","algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":77596,"name":"Morana Vitezic","orcid":"0000-0002-7994-9600","position":1,"is_corresponding":false},{"id":76166,"name":"Abel Ureta-Vidal","orcid":null,"position":2,"is_corresponding":false},{"id":2123,"name":"Richard Durbin","orcid":"0000-0002-9130-1006","position":4,"is_corresponding":false},{"id":18085,"name":"Kerstin Lindblad‐Toh","orcid":"0000-0001-8338-0253","position":5,"is_corresponding":false},{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":6,"is_corresponding":false},{"id":41930,"name":"Albert J. Vilella","orcid":"0000-0002-2005-2516","position":0,"is_corresponding":true}],"reference_count":27,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}