{"id":"https://openalex.org/W2950514289","doi":"https://doi.org/10.1093/bioinformatics/btw778","title":"Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses","display_name":"Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses","publication_year":2016,"publication_date":"2016-12-02","ids":{"openalex":"https://openalex.org/W2950514289","doi":"https://doi.org/10.1093/bioinformatics/btw778","mag":"2950514289","pmid":"https://pubmed.ncbi.nlm.nih.gov/28073758"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/980/25149954/btw778.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/980/25149954/btw778.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084338741","display_name":"Edwin Jacox","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/I159885104","display_name":"\u00c9cole Pratique des Hautes \u00c9tudes","ror":"https://ror.org/046b3cj80","country_code":"FR","type":"education","lineage":["https://openalex.org/I159885104","https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210105943","display_name":"Institut des Sciences de l'Evolution de Montpellier","ror":"https://ror.org/01cah1n37","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I2746051580","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210105943","https://openalex.org/I4210107625","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Edwin Jacox","raw_affiliation_strings":["ISE-M, Universit\u00e9 Montpellier, CNRS, IRD, EPHE, Montpellier, France","UMR ISEM - Institut des Sciences de l'Evolution de Montpellier (Place E. Bataillon CC 064 34095 Montpellier Cedex 05 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ISE-M, Universit\u00e9 Montpellier, CNRS, IRD, EPHE, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I159885104","https://openalex.org/I4210166444","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"UMR ISEM - Institut des Sciences de l'Evolution de Montpellier (Place E. Bataillon CC 064 34095 Montpellier Cedex 05 - France)","institution_ids":["https://openalex.org/I4210105943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030931327","display_name":"Mathias Weller","orcid":"https://orcid.org/0000-0002-9653-3690"},"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Mathias Weller","raw_affiliation_strings":["Institut de Biologie Computationnelle (IBC), Montpellier, France","LIRMM, Universit\u00e9 Montpellier, CNRS, Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Biologie Computationnelle (IBC), Montpellier, France","institution_ids":[]},{"raw_affiliation_string":"LIRMM, Universit\u00e9 Montpellier, CNRS, Montpellier, France","institution_ids":["https://openalex.org/I4210101743","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026210731","display_name":"\u00c9ric Tannier","orcid":"https://orcid.org/0000-0002-3681-7536"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210104684","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Eric Tannier","raw_affiliation_strings":["INRIA Rh\u00f4ne-Alpes, LBBE, Universit\u00e9 Lyon 1, Lyon, France","Artificial Evolution and Computational Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Rh\u00f4ne-Alpes, LBBE, Universit\u00e9 Lyon 1, Lyon, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1326498283","https://openalex.org/I4210135640"]},{"raw_affiliation_string":"Artificial Evolution and Computational Biology","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057284934","display_name":"C\u00e9line Scornavacca","orcid":"https://orcid.org/0009-0004-0179-9771"},"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/I159885104","display_name":"\u00c9cole Pratique des Hautes \u00c9tudes","ror":"https://ror.org/046b3cj80","country_code":"FR","type":"education","lineage":["https://openalex.org/I159885104","https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210105943","display_name":"Institut des Sciences de l'Evolution de Montpellier","ror":"https://ror.org/01cah1n37","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I2746051580","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210105943","https://openalex.org/I4210107625","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Celine Scornavacca","raw_affiliation_strings":["ISE-M, Universit\u00e9 Montpellier, CNRS, IRD, EPHE, Montpellier, France","Institut de Biologie Computationnelle (IBC), Montpellier, France","UMR ISEM - Institut des Sciences de l'Evolution de Montpellier (Place E. Bataillon CC 064 34095 Montpellier Cedex 05 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ISE-M, Universit\u00e9 Montpellier, CNRS, IRD, EPHE, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I159885104","https://openalex.org/I4210166444","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Institut de Biologie Computationnelle (IBC), Montpellier, France","institution_ids":[]},{"raw_affiliation_string":"UMR ISEM - Institut des Sciences de l'Evolution de Montpellier (Place E. Bataillon CC 064 34095 Montpellier Cedex 05 - France)","institution_ids":["https://openalex.org/I4210105943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5057284934"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I4210105943","https://openalex.org/I4210166444"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0251,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.79120347,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"7","first_page":"980","last_page":"987"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.909600019454956,"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":0.909600019454956,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.07930000126361847,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.00279999990016222,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/parameterized-complexity","display_name":"Parameterized complexity","score":0.656075119972229},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6528948545455933},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6386867165565491},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5955814123153687},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.5948473215103149},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5812100172042847},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5730781555175781},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.5375753045082092},{"id":"https://openalex.org/keywords/binary-tree","display_name":"Binary tree","score":0.5154081583023071},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5008623600006104},{"id":"https://openalex.org/keywords/exponential-growth","display_name":"Exponential growth","score":0.46506908535957336},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4257271885871887},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32185372710227966},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31089213490486145},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2992243766784668},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.2358526587486267},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2025354504585266},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10977551341056824}],"concepts":[{"id":"https://openalex.org/C165464430","wikidata":"https://www.wikidata.org/wiki/Q1570441","display_name":"Parameterized complexity","level":2,"score":0.656075119972229},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6528948545455933},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6386867165565491},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5955814123153687},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.5948473215103149},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5812100172042847},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5730781555175781},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.5375753045082092},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.5154081583023071},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5008623600006104},{"id":"https://openalex.org/C75235859","wikidata":"https://www.wikidata.org/wiki/Q582659","display_name":"Exponential growth","level":2,"score":0.46506908535957336},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4257271885871887},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32185372710227966},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31089213490486145},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2992243766784668},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.2358526587486267},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2025354504585266},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10977551341056824},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020560","descriptor_name":"Proteobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020560","descriptor_name":"Proteobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020560","descriptor_name":"Proteobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/980/25149954/btw778.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28073758","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28073758","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-01526643v1","is_oa":false,"landing_page_url":"https://hal.science/hal-01526643","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2017, 33 (7), pp.980-987. ⟨10.1093/bioinformatics/btw778⟩","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/980/25149954/btw778.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5147357711","display_name":"Approche de phylog\u00e9nie int\u00e9grative pour la reconstruction de g\u00e9nomes ancestraux","funder_award_id":"ANR-10-BINF-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6115547468","display_name":"Institut de biologie Computationnelle","funder_award_id":"ANR-11-BINF-0002","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W193910531","https://openalex.org/W1519266993","https://openalex.org/W1641026754","https://openalex.org/W1980050219","https://openalex.org/W2013067928","https://openalex.org/W2070579299","https://openalex.org/W2088979937","https://openalex.org/W2103849916","https://openalex.org/W2104398544","https://openalex.org/W2105669285","https://openalex.org/W2111211467","https://openalex.org/W2112755610","https://openalex.org/W2119900532","https://openalex.org/W2125359798","https://openalex.org/W2131944877","https://openalex.org/W2132318428","https://openalex.org/W2141052558","https://openalex.org/W2148231054","https://openalex.org/W2149681675","https://openalex.org/W2151070329","https://openalex.org/W2159545652","https://openalex.org/W2159579403","https://openalex.org/W2287141830","https://openalex.org/W2341168710","https://openalex.org/W2343945200","https://openalex.org/W2557536938","https://openalex.org/W4233815609","https://openalex.org/W4285719527","https://openalex.org/W6678804063"],"related_works":["https://openalex.org/W2051058708","https://openalex.org/W1494268238","https://openalex.org/W154868527","https://openalex.org/W1983207144","https://openalex.org/W2490706771","https://openalex.org/W2480116122","https://openalex.org/W4255576661","https://openalex.org/W1516574938","https://openalex.org/W2625725254","https://openalex.org/W2897404811"],"abstract_inverted_index":{"Summary:":[0],"Gene":[1],"trees":[2],"reconstructed":[3],"from":[4,118],"sequence":[5,120],"alignments":[6],"contain":[7],"poorly":[8],"supported":[9],"branches":[10,67,109,139],"when":[11],"the":[12,16,30,44,48,65,102,105,111,119,124,133,137,146,165,170,207,221],"phylogenetic":[13],"signal":[14,31],"in":[15,80,98,185],"sequences":[17],"is":[18,28,68,104,210],"insufficient":[19],"to":[20,41,82,94,158,187],"determine":[21],"them":[22],"all.":[23],"When":[24],"a":[25,53,59,156,199,204],"species":[26],"tree":[27,61,113,135],"available,":[29],"of":[32,36,47,58,107,110,127,129,132,172],"gains":[33],"and":[34,86,178,203,213,228],"losses":[35],"genes":[37],"can":[38,230],"be":[39,231],"used":[40],"correctly":[42],"resolve":[43],"unsupported":[45,66],"parts":[46],"gene":[49,77,83,112,134],"history.":[50],"However":[51],"finding":[52],"most":[54],"parsimonious":[55],"binary":[56],"resolution":[57],"non-binary":[60],"obtained":[62],"by":[63,150],"contracting":[64],"NP-hard":[69],"if":[70],"transfer":[71],"events":[72],"are":[73,183,243],"considered":[74],"as":[75],"possible":[76],"scale":[78],"events,":[79],"addition":[81],"origination,":[84],"duplication":[85],"loss.":[87],"We":[88,154,168],"propose":[89,155],"an":[90,151],"exact,":[91],"parameterized":[92],"algorithm":[93,149,216],"solve":[95],"this":[96,173],"problem":[97],"single-exponential":[99],"time,":[100],"where":[101],"parameter":[103],"number":[106,126],"connected":[108],"that":[114,206],"show":[115,169],"low":[116],"support":[117],"alignment":[121],"or,":[122],"equivalently,":[123],"maximum":[125],"children":[128],"any":[130],"node":[131],"once":[136],"low-support":[138],"have":[140],"been":[141,218],"collapsed.":[142],"This":[143],"improves":[144],"on":[145,164,175],"best":[147],"known":[148],"exponential":[152],"factor.":[153],"way":[157],"choose":[159],"among":[160],"optimal":[161],"solutions":[162],"based":[163],"available":[166,225,244],"information.":[167],"usability":[171],"principle":[174],"several":[176,188],"simulated":[177],"biological":[179],"datasets.":[180],"The":[181],"results":[182],"comparable":[184],"quality":[186],"other":[189],"tested":[190],"methods":[191],"having":[192],"similar":[193],"goals,":[194],"but":[195],"our":[196],"approach":[197],"provides":[198],"lower":[200],"running":[201],"time":[202],"guarantee":[205],"produced":[208],"solution":[209],"optimal.":[211],"Availability":[212],"Implementation:":[214],"Our":[215],"has":[217],"integrated":[219],"into":[220],"ecceTERA":[222],"phylogeny":[223],"package,":[224],"at":[226,234,245],"http://mbb.univ-montp2.fr/MBB/download_sources/16__ecceTERA":[227],"which":[229],"run":[232],"online":[233],"http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera":[235],".":[236],"Contact:":[237],"celine.scornavacca@umontpellier.fr.":[238],"Supplementary":[239,241],"information:":[240],"data":[242],"Bioinformatics":[246],"online.":[247]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}