{"doi":"10.1093/bioinformatics/btm193","title":"Automatic genome-wide reconstruction of phylogenetic gene trees","abstract":"<h4>Unlabelled</h4>Gene duplication and divergence is a major evolutionary force. Despite the growing number of fully sequenced genomes, methods for investigating these events on a genome-wide scale are still in their infancy. Here, we present SYNERGY, a novel and scalable algorithm that uses sequence similarity and a given species phylogeny to reconstruct the underlying evolutionary history of all genes in a large group of species. In doing so, SYNERGY resolves homology relations and accurately distinguishes orthologs from paralogs. We applied our approach to a set of nine fully sequenced fungal genomes spanning 150 million years, generating a genome-wide catalog of orthologous groups and corresponding gene trees. Our results are highly accurate when compared to a manually curated gold standard, and are robust to the quality of input according to a novel jackknife confidence scoring. The reconstructed gene trees provide a comprehensive view of gene evolution on a genomic scale. Our approach can be applied to any set of sequenced eukaryotic species with a known phylogeny, and opens the way to systematic studies of the evolution of individual genes, molecular systems and whole genomes.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2007,"id":11077,"datarank":7.030221419866961,"base_score":4.941642422609304,"endowment":4.941642422609304,"self_citation_contribution":0.7412463633913957,"citation_network_contribution":6.288975056475565,"self_endowment_contribution":0.7412463633913957,"citer_contribution":6.288975056475565,"corpus_percentile":null,"corpus_rank":null,"citation_count":139,"citer_count":131,"citers_with_citation_signal":114,"citers_with_endowment":114,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0459,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2007-07-01","algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":54422,"name":"Avi Pfeffer","orcid":"0000-0002-6724-2640","position":1,"is_corresponding":false},{"id":11210,"name":"Nir Friedman","orcid":"0000-0002-9678-3550","position":2,"is_corresponding":false},{"id":29633,"name":"Prisca Liberali","orcid":"0000-0003-0695-6081","position":3,"is_corresponding":false},{"id":29491,"name":"Ilan Wapinski","orcid":null,"position":0,"is_corresponding":true}],"reference_count":29,"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":[]}