{"id":"https://openalex.org/W4413780499","doi":"https://doi.org/10.1093/bioinformatics/btaf479","title":"FUSE-PhyloTree: linking functions and sequence conservation modules of a protein family through phylogenomic analysis","display_name":"FUSE-PhyloTree: linking functions and sequence conservation modules of a protein family through phylogenomic analysis","publication_year":2025,"publication_date":"2025-08-26","ids":{"openalex":"https://openalex.org/W4413780499","doi":"https://doi.org/10.1093/bioinformatics/btaf479","pmid":"https://pubmed.ncbi.nlm.nih.gov/40875493"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf479","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf479","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf479/64149622/btaf479.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf479/64149622/btaf479.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053700598","display_name":"Olivier Dennler","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Olivier Dennler","raw_affiliation_strings":["Univ Rennes, INSERM, EHESP, Institut de Recherche en Sant\u00e9 Environnement et Travail (IRSET) - UMR_S 1085 , 9 avenue du Prof. L\u00e9on Bernard , Rennes, F-35000,","Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Univ Rennes, Inserm, EHESP, IRSET, UMR_S 1085, Rennes, France"],"raw_orcid":"https://orcid.org/0009-0005-2408-1102","affiliations":[{"raw_affiliation_string":"Univ Rennes, INSERM, EHESP, Institut de Recherche en Sant\u00e9 Environnement et Travail (IRSET) - UMR_S 1085 , 9 avenue du Prof. L\u00e9on Bernard , Rennes, F-35000,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210108239","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, IRSET, UMR_S 1085, Rennes, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I56067802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116877415","display_name":"Elisa Chenel","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Elisa Chenel","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055528856","display_name":"F Coste","orcid":"https://orcid.org/0000-0001-9134-6557"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Fran\u00e7ois Coste","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France"],"raw_orcid":"https://orcid.org/0000-0001-9134-6557","affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090186467","display_name":"Samuel Blanquart","orcid":"https://orcid.org/0000-0002-1408-3068"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Samuel Blanquart","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006160656","display_name":"Catherine Belleann\u00e9e","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Catherine Belleann\u00e9e","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046388663","display_name":"Nathalie Th\u00e9ret","orcid":"https://orcid.org/0000-0002-5857-7828"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Nathalie Th\u00e9ret","raw_affiliation_strings":["Univ Rennes, INSERM, EHESP, Institut de Recherche en Sant\u00e9 Environnement et Travail (IRSET) - UMR_S 1085 , 9 avenue du Prof. L\u00e9on Bernard , Rennes, F-35000,","Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Univ Rennes, Inserm, EHESP, IRSET, UMR_S 1085, Rennes, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ Rennes, INSERM, EHESP, Institut de Recherche en Sant\u00e9 Environnement et Travail (IRSET) - UMR_S 1085 , 9 avenue du Prof. L\u00e9on Bernard , Rennes, F-35000,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210108239","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA - UMR 6074 , Rennes, F-35000,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, IRSET, UMR_S 1085, Rennes, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I56067802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046388663","https://openalex.org/A5053700598","https://openalex.org/A5055528856","https://openalex.org/A5090186467"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I2802519937","https://openalex.org/I4210108239","https://openalex.org/I56067802"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12804381,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6158000230789185,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6158000230789185,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.05990000069141388,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.05649999901652336,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fuse","display_name":"Fuse (electrical)","score":0.6095920205116272},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5828273296356201},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4952212870121002},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4681316614151001},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4204961657524109},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4078245759010315},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3894907534122467},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3869704604148865},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2577096223831177},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.24747326970100403},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14097905158996582},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0798751711845398}],"concepts":[{"id":"https://openalex.org/C141353440","wikidata":"https://www.wikidata.org/wiki/Q182221","display_name":"Fuse (electrical)","level":2,"score":0.6095920205116272},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5828273296356201},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4952212870121002},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4681316614151001},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4204961657524109},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4078245759010315},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3894907534122467},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3869704604148865},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2577096223831177},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.24747326970100403},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14097905158996582},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0798751711845398},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf479","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf479","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf479/64149622/btaf479.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40875493","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40875493","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-05238604v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05238604","pdf_url":"https://hal.science/hal-05238604/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2025, pp.btaf479. &#x27E8;10.1093/bioinformatics/btaf479&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf479","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf479","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf479/64149622/btaf479.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413780499.pdf","grobid_xml":"https://content.openalex.org/works/W4413780499.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W1525517788"],"abstract_inverted_index":{"SUMMARY:":[0],"FUSE-PhyloTree":[1,26,84,115],"is":[2,66,116],"a":[3,18,82,86],"phylogenomic":[4],"analysis":[5,35],"software":[6,127],"for":[7],"identifying":[8],"local":[9,40,51],"sequence":[10,34,41,53,93,106],"conservation":[11,42],"associated":[12],"with":[13,36,90,104],"the":[14,45,56,59,69,100,125],"different":[15],"functions":[16,65,103],"of":[17,58,102],"multi-functional":[19],"(e.g.":[20],"paralogous":[21],"or":[22],"multi-domain)":[23],"protein":[24,64],"family.":[25],"introduces":[27],"an":[28],"original":[29],"approach":[30],"that":[31],"combines":[32],"advanced":[33],"phylogenetic":[37,71,75],"methods.":[38],"First,":[39],"modules":[43,61,94],"within":[44,68],"family":[46],"are":[47,136],"identified":[48],"using":[49,73],"partial":[50],"multiple":[52],"alignment.":[54],"Next,":[55],"evolution":[57],"detected":[60],"and":[62,77,95,120,134,140],"known":[63],"inferred":[67],"family's":[70],"tree":[72,88],"three-level":[74],"reconciliation":[76],"ancestral":[78,96],"state":[79],"reconstruction.":[80],"As":[81],"result,":[83],"provides":[85],"gene":[87,97],"annotated":[89],"both":[91],"predicted":[92],"functions,":[98],"enabling":[99],"association":[101],"specific":[105],"regions":[107],"based":[108],"on":[109],"their":[110],"co-emergence.":[111],"AVAILABILITY":[112],"AND":[113],"IMPLEMENTATION:":[114],"provided":[117],"as":[118],"Docker":[119],"Singularity":[121],"images":[122],"including":[123],"all":[124],"required":[126],"tools.":[128],"Images,":[129],"source":[130],"code,":[131],"test":[132],"data,":[133],"documentation":[135],"available":[137],"at":[138],"https://github.com/OcMalde/fuse-phylotree":[139],"https://zenodo.org/records/15855068.":[141]},"counts_by_year":[],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
