{"id":"https://openalex.org/W2151781607","doi":"https://doi.org/10.1093/bioinformatics/btu463","title":"Polytomy refinement for the correction of dubious duplications in gene trees","display_name":"Polytomy refinement for the correction of dubious duplications in gene trees","publication_year":2014,"publication_date":"2014-08-22","ids":{"openalex":"https://openalex.org/W2151781607","doi":"https://doi.org/10.1093/bioinformatics/btu463","mag":"2151781607","pmid":"https://pubmed.ncbi.nlm.nih.gov/25161242"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu463","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu463","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/17/i519/17150242/btu463.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/30/17/i519/17150242/btu463.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016796629","display_name":"Manuel Lafond","orcid":"https://orcid.org/0000-0002-5305-7372"},"institutions":[{"id":"https://openalex.org/I11039511","display_name":"University of Bergamo","ror":"https://ror.org/02mbd5571","country_code":"IT","type":"education","lineage":["https://openalex.org/I11039511"]},{"id":"https://openalex.org/I15057530","display_name":"Universit\u00e9 de Bordeaux","ror":"https://ror.org/057qpr032","country_code":"FR","type":"education","lineage":["https://openalex.org/I15057530"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I4210142254","display_name":"Laboratoire Bordelais de Recherche en Informatique","ror":"https://ror.org/03adqg323","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I15057530","https://openalex.org/I4210142254","https://openalex.org/I4210159245","https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I4210160189","display_name":"Institut Polytechnique de Bordeaux","ror":"https://ror.org/054qv7y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA","FR","IT"],"is_corresponding":true,"raw_author_name":"Manuel Lafond","raw_affiliation_strings":["1 Department of Computer Science, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Quebec H3C 3J7, Canada, 2LaBRI, Universit\u00e9 Bordeaux 1, Bordeaux, France, 3Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A 1S6, Canada and 4Universit\u00e1 degli Studi di Bergamo, Bergamo 24129 IT, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Quebec H3C 3J7, Canada, 2LaBRI, Universit\u00e9 Bordeaux 1, Bordeaux, France, 3Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A 1S6, Canada and 4Universit\u00e1 degli Studi di Bergamo, Bergamo 24129 IT, Italy","institution_ids":["https://openalex.org/I11039511","https://openalex.org/I15057530","https://openalex.org/I18014758","https://openalex.org/I4210142254","https://openalex.org/I4210160189","https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063811688","display_name":"C\u00e9dric Chauve","orcid":"https://orcid.org/0000-0001-9837-1878"},"institutions":[{"id":"https://openalex.org/I11039511","display_name":"University of Bergamo","ror":"https://ror.org/02mbd5571","country_code":"IT","type":"education","lineage":["https://openalex.org/I11039511"]},{"id":"https://openalex.org/I15057530","display_name":"Universit\u00e9 de Bordeaux","ror":"https://ror.org/057qpr032","country_code":"FR","type":"education","lineage":["https://openalex.org/I15057530"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I4210142254","display_name":"Laboratoire Bordelais de Recherche en Informatique","ror":"https://ror.org/03adqg323","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I15057530","https://openalex.org/I4210142254","https://openalex.org/I4210159245","https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I4210160189","display_name":"Institut Polytechnique de Bordeaux","ror":"https://ror.org/054qv7y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA","FR","IT"],"is_corresponding":false,"raw_author_name":"Cedric Chauve","raw_affiliation_strings":["1 Department of Computer Science, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Quebec H3C 3J7, Canada, 2LaBRI, Universit\u00e9 Bordeaux 1, Bordeaux, France, 3Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A 1S6, Canada and 4Universit\u00e1 degli Studi di Bergamo, Bergamo 24129 IT, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Quebec H3C 3J7, Canada, 2LaBRI, Universit\u00e9 Bordeaux 1, Bordeaux, France, 3Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A 1S6, Canada and 4Universit\u00e1 degli Studi di Bergamo, Bergamo 24129 IT, Italy","institution_ids":["https://openalex.org/I11039511","https://openalex.org/I15057530","https://openalex.org/I18014758","https://openalex.org/I4210142254","https://openalex.org/I4210160189","https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059320347","display_name":"Riccardo Dondi","orcid":"https://orcid.org/0000-0002-6124-2965"},"institutions":[{"id":"https://openalex.org/I11039511","display_name":"University of Bergamo","ror":"https://ror.org/02mbd5571","country_code":"IT","type":"education","lineage":["https://openalex.org/I11039511"]},{"id":"https://openalex.org/I15057530","display_name":"Universit\u00e9 de Bordeaux","ror":"https://ror.org/057qpr032","country_code":"FR","type":"education","lineage":["https://openalex.org/I15057530"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I4210142254","display_name":"Laboratoire Bordelais de Recherche en Informatique","ror":"https://ror.org/03adqg323","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I15057530","https://openalex.org/I4210142254","https://openalex.org/I4210159245","https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I4210160189","display_name":"Institut Polytechnique de Bordeaux","ror":"https://ror.org/054qv7y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA","FR","IT"],"is_corresponding":false,"raw_author_name":"Riccardo Dondi","raw_affiliation_strings":["1 Department of Computer Science, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Quebec H3C 3J7, Canada, 2LaBRI, Universit\u00e9 Bordeaux 1, Bordeaux, France, 3Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A 1S6, Canada and 4Universit\u00e1 degli Studi di Bergamo, Bergamo 24129 IT, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Quebec H3C 3J7, Canada, 2LaBRI, Universit\u00e9 Bordeaux 1, Bordeaux, France, 3Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A 1S6, Canada and 4Universit\u00e1 degli Studi di Bergamo, Bergamo 24129 IT, Italy","institution_ids":["https://openalex.org/I11039511","https://openalex.org/I15057530","https://openalex.org/I18014758","https://openalex.org/I4210142254","https://openalex.org/I4210160189","https://openalex.org/I70931966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041470344","display_name":"Nadia El-Mabrouk","orcid":"https://orcid.org/0000-0002-5385-1015"},"institutions":[{"id":"https://openalex.org/I11039511","display_name":"University of Bergamo","ror":"https://ror.org/02mbd5571","country_code":"IT","type":"education","lineage":["https://openalex.org/I11039511"]},{"id":"https://openalex.org/I15057530","display_name":"Universit\u00e9 de Bordeaux","ror":"https://ror.org/057qpr032","country_code":"FR","type":"education","lineage":["https://openalex.org/I15057530"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I4210142254","display_name":"Laboratoire Bordelais de Recherche en Informatique","ror":"https://ror.org/03adqg323","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I15057530","https://openalex.org/I4210142254","https://openalex.org/I4210159245","https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I4210160189","display_name":"Institut Polytechnique de Bordeaux","ror":"https://ror.org/054qv7y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA","FR","IT"],"is_corresponding":true,"raw_author_name":"Nadia El-Mabrouk","raw_affiliation_strings":["1 Department of Computer Science, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Quebec H3C 3J7, Canada, 2LaBRI, Universit\u00e9 Bordeaux 1, Bordeaux, France, 3Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A 1S6, Canada and 4Universit\u00e1 degli Studi di Bergamo, Bergamo 24129 IT, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Quebec H3C 3J7, Canada, 2LaBRI, Universit\u00e9 Bordeaux 1, Bordeaux, France, 3Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A 1S6, Canada and 4Universit\u00e1 degli Studi di Bergamo, Bergamo 24129 IT, Italy","institution_ids":["https://openalex.org/I11039511","https://openalex.org/I15057530","https://openalex.org/I18014758","https://openalex.org/I4210142254","https://openalex.org/I4210160189","https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5016796629","https://openalex.org/A5041470344"],"corresponding_institution_ids":["https://openalex.org/I11039511","https://openalex.org/I15057530","https://openalex.org/I18014758","https://openalex.org/I4210142254","https://openalex.org/I4210160189","https://openalex.org/I70931966"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9098,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.73660669,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"17","first_page":"i519","last_page":"i526"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.38850000500679016,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.38850000500679016,"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/T10885","display_name":"Gene expression and cancer classification","score":0.25189998745918274,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.10429999977350235,"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/source-code","display_name":"Source code","score":0.6185470819473267},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6073311567306519},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6047600507736206},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.552906334400177},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.5230972766876221},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5033144354820251},{"id":"https://openalex.org/keywords/bounded-function","display_name":"Bounded function","score":0.4883667826652527},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.47982096672058105},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4604286849498749},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.46033036708831787},{"id":"https://openalex.org/keywords/binary-tree","display_name":"Binary tree","score":0.4284248948097229},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.42544832825660706},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4113013744354248},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3871362805366516},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.38503995537757874},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.374420702457428},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35164886713027954},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3126472234725952},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30417993664741516},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2508898675441742},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.17487984895706177},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13598957657814026},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.11527812480926514},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10880467295646667},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.0803273618221283}],"concepts":[{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6185470819473267},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6073311567306519},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6047600507736206},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.552906334400177},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.5230972766876221},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5033144354820251},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.4883667826652527},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.47982096672058105},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4604286849498749},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.46033036708831787},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.4284248948097229},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.42544832825660706},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4113013744354248},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3871362805366516},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.38503995537757874},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.374420702457428},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35164886713027954},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3126472234725952},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30417993664741516},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2508898675441742},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.17487984895706177},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13598957657814026},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.11527812480926514},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10880467295646667},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.0803273618221283},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005399","descriptor_name":"Fishes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005399","descriptor_name":"Fishes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005399","descriptor_name":"Fishes","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btu463","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu463","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/17/i519/17150242/btu463.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:25161242","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25161242","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:CiteSeerX.psu:10.1.1.639.8889","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.639.8889","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.iro.umontreal.ca/~mabrouk/Publications/correction-nad.pdf","raw_type":"text"},{"id":"pmh:oai:aisberg.unibg.it:10446/32091","is_oa":true,"landing_page_url":"http://hdl.handle.net/10446/32091","pdf_url":null,"source":{"id":"https://openalex.org/S4377196347","display_name":"Aisberg (University of Bergamo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11039511","host_organization_name":"University of Bergamo","host_organization_lineage":["https://openalex.org/I11039511"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4147916","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/btu463","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu463","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu463","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/17/i519/17150242/btu463.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/G1596043999","display_name":null,"funder_award_id":"PRIN 2010-2011","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G3653413569","display_name":null,"funder_award_id":"2010-2011","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G4244614701","display_name":null,"funder_award_id":"H41J12000190001","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G5458840301","display_name":null,"funder_award_id":"PRIN 2010","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334841","display_name":"Fonds de recherche du Qu\u00e9bec \u2013 Nature et technologies","ror":"https://ror.org/00b9f9778"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2151781607.pdf","grobid_xml":"https://content.openalex.org/works/W2151781607.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W39630659","https://openalex.org/W598887167","https://openalex.org/W1523611852","https://openalex.org/W1527695627","https://openalex.org/W1537213512","https://openalex.org/W1576387209","https://openalex.org/W1799812931","https://openalex.org/W1931647778","https://openalex.org/W1972157500","https://openalex.org/W1988471037","https://openalex.org/W2004575303","https://openalex.org/W2015906942","https://openalex.org/W2022472106","https://openalex.org/W2024812560","https://openalex.org/W2041346050","https://openalex.org/W2061646232","https://openalex.org/W2065375138","https://openalex.org/W2088392408","https://openalex.org/W2095829109","https://openalex.org/W2097706568","https://openalex.org/W2102020547","https://openalex.org/W2102424972","https://openalex.org/W2103546861","https://openalex.org/W2105669285","https://openalex.org/W2112537533","https://openalex.org/W2113234327","https://openalex.org/W2119801041","https://openalex.org/W2123169853","https://openalex.org/W2132023322","https://openalex.org/W2133880039","https://openalex.org/W2135398177","https://openalex.org/W2137015675","https://openalex.org/W2137604740","https://openalex.org/W2138040811","https://openalex.org/W2144106734","https://openalex.org/W2146058063","https://openalex.org/W2149049580","https://openalex.org/W2151070329","https://openalex.org/W2157360426","https://openalex.org/W2165484374","https://openalex.org/W2206883064","https://openalex.org/W4210347168","https://openalex.org/W4285719527","https://openalex.org/W6631222105","https://openalex.org/W6674647444","https://openalex.org/W6680149418","https://openalex.org/W6680365775","https://openalex.org/W6681042170"],"related_works":["https://openalex.org/W2358841807","https://openalex.org/W3033962221","https://openalex.org/W2770371694","https://openalex.org/W2737894786","https://openalex.org/W2491277646","https://openalex.org/W1979781836","https://openalex.org/W1992055950","https://openalex.org/W3091576183","https://openalex.org/W4319999454","https://openalex.org/W2102727825"],"abstract_inverted_index":{"MOTIVATION:":[0],"Large-scale":[1],"methods":[2],"for":[3,12,104,138],"inferring":[4],"gene":[5,10,44,57,69,117],"trees":[6,11,22,45,118],"are":[7,46,49,147,155],"error-prone.":[8],"Correcting":[9],"weakly":[13],"supported":[14,51],"features":[15],"often":[16],"results":[17],"in":[18,43,67,79,144],"non-binary":[19],"trees,":[20],"i.e.":[21],"with":[23,101],"polytomies,":[24],"thus":[25],"raising":[26],"the":[27,53,62,73,80,120,139,145],"natural":[28],"question":[29],"of":[30,55,64,75,114],"refining":[31,65],"such":[32],"polytomies":[33,66],"into":[34],"binary":[35],"trees.":[36],"A":[37],"feature":[38],"pointing":[39],"toward":[40],"potential":[41],"errors":[42],"duplications":[47,78],"that":[48,85],"not":[50],"by":[52],"presence":[54],"multiple":[56],"copies.":[58],"RESULTS:":[59],"We":[60,83,96,107],"introduce":[61],"problem":[63,87],"a":[68,92,98,112],"tree":[70],"while":[71],"minimizing":[72],"number":[74],"created":[76],"non-apparent":[77],"resulting":[81],"tree.":[82],"show":[84],"this":[86],"can":[88],"be":[89],"described":[90,143],"as":[91],"graph-theoretical":[93],"optimization":[94],"problem.":[95],"provide":[97],"bounded":[99],"heuristic":[100],"guaranteed":[102],"optimality":[103],"well-characterized":[105],"instances.":[106],"apply":[108],"our":[109],"algorithm":[110],"to":[111,123,127],"set":[113],"ray-finned":[115],"fish":[116],"from":[119],"Ensembl":[121],"database":[122],"illustrate":[124],"its":[125],"ability":[126],"correct":[128],"dubious":[129],"duplications.":[130],"AVAILABILITY":[131],"AND":[132],"IMPLEMENTATION:":[133],"The":[134],"C++":[135],"source":[136],"code":[137],"algorithms":[140],"and":[141],"simulations":[142],"article":[146],"available":[148,156],"at":[149,157],"http://www-ens.iro.umontreal.ca/~lafonman/software.php.":[150],"SUPPLEMENTARY":[151],"INFORMATION:":[152],"Supplementary":[153],"data":[154],"Bioinformatics":[158],"online.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}