{"id":"https://openalex.org/W2149681675","doi":"https://doi.org/10.1093/bioinformatics/btu728","title":"Joint amalgamation of most parsimonious reconciled gene trees","display_name":"Joint amalgamation of most parsimonious reconciled gene trees","publication_year":2014,"publication_date":"2014-11-06","ids":{"openalex":"https://openalex.org/W2149681675","doi":"https://doi.org/10.1093/bioinformatics/btu728","mag":"2149681675","pmid":"https://pubmed.ncbi.nlm.nih.gov/25380957"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu728","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu728","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/841/49011277/bioinformatics_31_6_841.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/841/49011277/bioinformatics_31_6_841.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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/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":["1 ISEM, UM2-CNRS-IRD, Place Eug\u00e8ne Bataillon 34095 Montpellier, France, 2Institut de Biologie Computationnelle (IBC), 95 rue de la Gal\u00e9ra, 34095 Montpellier, France and 3ELTE-MTA \u2018Lend\u00fclet\u2019 Biophysics Research Group 1117 Bp., P\u00e1zm\u00e1ny P. stny. 1A., Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 ISEM, UM2-CNRS-IRD, Place Eug\u00e8ne Bataillon 34095 Montpellier, France, 2Institut de Biologie Computationnelle (IBC), 95 rue de la Gal\u00e9ra, 34095 Montpellier, France and 3ELTE-MTA \u2018Lend\u00fclet\u2019 Biophysics Research Group 1117 Bp., P\u00e1zm\u00e1ny P. stny. 1A., Budapest, Hungary","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210105943","https://openalex.org/I4210166444"]}]},{"author_position":"middle","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/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":["1 ISEM, UM2-CNRS-IRD, Place Eug\u00e8ne Bataillon 34095 Montpellier, France, 2Institut de Biologie Computationnelle (IBC), 95 rue de la Gal\u00e9ra, 34095 Montpellier, France and 3ELTE-MTA \u2018Lend\u00fclet\u2019 Biophysics Research Group 1117 Bp., P\u00e1zm\u00e1ny P. stny. 1A., Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 ISEM, UM2-CNRS-IRD, Place Eug\u00e8ne Bataillon 34095 Montpellier, France, 2Institut de Biologie Computationnelle (IBC), 95 rue de la Gal\u00e9ra, 34095 Montpellier, France and 3ELTE-MTA \u2018Lend\u00fclet\u2019 Biophysics Research Group 1117 Bp., P\u00e1zm\u00e1ny P. stny. 1A., Budapest, Hungary","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210105943","https://openalex.org/I4210166444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013858021","display_name":"Gergely J. Sz\u00f6ll\u0151si","orcid":"https://orcid.org/0000-0002-8556-845X"},"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/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":"Gergely J. Sz\u00f6ll\u0151si","raw_affiliation_strings":["1 ISEM, UM2-CNRS-IRD, Place Eug\u00e8ne Bataillon 34095 Montpellier, France, 2Institut de Biologie Computationnelle (IBC), 95 rue de la Gal\u00e9ra, 34095 Montpellier, France and 3ELTE-MTA \u2018Lend\u00fclet\u2019 Biophysics Research Group 1117 Bp., P\u00e1zm\u00e1ny P. stny. 1A., Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 ISEM, UM2-CNRS-IRD, Place Eug\u00e8ne Bataillon 34095 Montpellier, France, 2Institut de Biologie Computationnelle (IBC), 95 rue de la Gal\u00e9ra, 34095 Montpellier, France and 3ELTE-MTA \u2018Lend\u00fclet\u2019 Biophysics Research Group 1117 Bp., P\u00e1zm\u00e1ny P. stny. 1A., Budapest, Hungary","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210105943","https://openalex.org/I4210166444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5013858021","https://openalex.org/A5057284934"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210105943","https://openalex.org/I4210166444"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.5995,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.90528101,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"31","issue":"6","first_page":"841","last_page":"848"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8949000239372253,"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":0.8949000239372253,"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":0.093299999833107,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.0017000000225380063,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/tera","display_name":"Tera-","score":0.7439217567443848},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6018027067184448},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5969743132591248},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5129096508026123},{"id":"https://openalex.org/keywords/maximum-parsimony","display_name":"Maximum parsimony","score":0.5116105675697327},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4803653657436371},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4574645161628723},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4528995752334595},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.43910133838653564},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33627527952194214},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33485448360443115},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32881078124046326},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29837697744369507},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24988406896591187},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24832817912101746},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14579111337661743}],"concepts":[{"id":"https://openalex.org/C2775904623","wikidata":"https://www.wikidata.org/wiki/Q108529","display_name":"Tera-","level":2,"score":0.7439217567443848},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6018027067184448},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5969743132591248},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5129096508026123},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.5116105675697327},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4803653657436371},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4574645161628723},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4528995752334595},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.43910133838653564},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33627527952194214},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33485448360443115},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32881078124046326},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29837697744369507},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24988406896591187},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24832817912101746},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14579111337661743},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000145","qualifier_name":"classification","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":"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","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":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btu728","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu728","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/841/49011277/bioinformatics_31_6_841.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25380957","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25380957","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:real.mtak.hu:29003","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400081","display_name":"Repository of the Academy's Library (Library of the Hungarian Academy of Sciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210140733","host_organization_name":"Library and Information Centre of the Hungarian Academy of Sciences","host_organization_lineage":["https://openalex.org/I4210140733"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.796.9871","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.796.9871","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/49/e9/btu728.PMC4380024.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:hal-02154935v1","is_oa":false,"landing_page_url":"https://hal.science/hal-02154935","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, 2015, 31 (6), pp.841-848. &#x27E8;10.1093/bioinformatics/btu728&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4380024","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4380024","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu728","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu728","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/841/49011277/bioinformatics_31_6_841.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G1839390385","display_name":"Assembling genome history from gene stories: Phylogeny aware genome scale inference of ancestral traits  and ancient environments","funder_award_id":"618438","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2122184555","display_name":null,"funder_award_id":"-2012-0001","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4455444033","display_name":null,"funder_award_id":"ANR-10-BINF-01-02","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"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/G7240651115","display_name":null,"funder_award_id":"ANR-10","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G945463265","display_name":null,"funder_award_id":"-2012-0001","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149681675.pdf","grobid_xml":"https://content.openalex.org/works/W2149681675.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W157609093","https://openalex.org/W1774207464","https://openalex.org/W1897064680","https://openalex.org/W1972157500","https://openalex.org/W1992584622","https://openalex.org/W2013067928","https://openalex.org/W2032545157","https://openalex.org/W2039334367","https://openalex.org/W2100099557","https://openalex.org/W2102424972","https://openalex.org/W2104398544","https://openalex.org/W2105669285","https://openalex.org/W2109432203","https://openalex.org/W2111211467","https://openalex.org/W2112537533","https://openalex.org/W2112755610","https://openalex.org/W2120836981","https://openalex.org/W2131944877","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2133880039","https://openalex.org/W2138113680","https://openalex.org/W2144454528","https://openalex.org/W2145608399","https://openalex.org/W2148231054","https://openalex.org/W2148698435","https://openalex.org/W2148818018","https://openalex.org/W2149582283","https://openalex.org/W2151070329","https://openalex.org/W2157360426","https://openalex.org/W2159545652","https://openalex.org/W2159579403","https://openalex.org/W2163627198","https://openalex.org/W2166106146","https://openalex.org/W2170753094","https://openalex.org/W2175974175","https://openalex.org/W6606317737","https://openalex.org/W6677017098","https://openalex.org/W6685859578"],"related_works":["https://openalex.org/W2520823390","https://openalex.org/W4300265711","https://openalex.org/W2963820820","https://openalex.org/W2963207658","https://openalex.org/W2362218761","https://openalex.org/W2375151634","https://openalex.org/W2062354928","https://openalex.org/W2090308851","https://openalex.org/W2113708670","https://openalex.org/W3146310663"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Traditionally,":[2],"gene":[3,44,101,126,136,178],"phylogenies":[4],"have":[5,36],"been":[6],"reconstructed":[7],"solely":[8],"on":[9,39,105,172],"the":[10,40,79,86,119,149,153,190,200],"basis":[11],"of":[12,75,78,118,135,175,189,202],"molecular":[13],"sequences;":[14],"this,":[15],"however,":[16],"often":[17],"does":[18],"not":[19],"provide":[20],"enough":[21],"information":[22,38],"to":[23,48,58],"distinguish":[24],"between":[25],"statistically":[26],"equivalent":[27],"relationships.":[28],"To":[29],"address":[30],"this":[31],"problem,":[32],"several":[33],"recent":[34],"methods":[35,55,164],"incorporated":[37],"species":[41,96,191],"phylogeny":[42],"in":[43,51,165,194,199,213],"tree":[45,97,102,192],"reconstruction,":[46],"leading":[47],"dramatic":[49],"improvements":[50],"accuracy.":[52],"Although":[53],"probabilistic":[54,155],"are":[56,64,230],"able":[57],"estimate":[59,74,117],"all":[60,124],"model":[61],"parameters":[62,76],"but":[63],"computationally":[65,69],"expensive,":[66],"parsimony":[67,94],"methods\u2014generally":[68],"more":[70],"efficient\u2014require":[71],"a":[72,93,106,133,139,173,195],"prior":[73],"and":[77,112,160,168,207],"statistical":[80],"support.":[81],"Results:":[82],"Here,":[83],"we":[84,144,184],"present":[85],"Tree":[87],"Estimation":[88],"using":[89],"Reconciliation":[90],"(TERA)":[91],"algorithm,":[92],"based,":[95],"aware":[98],"method":[99,156],"for":[100],"reconstruction":[103],"based":[104],"scoring":[107],"scheme":[108],"combining":[109],"duplication,":[110],"transfer":[111,204],"loss":[113],"costs":[114],"with":[115],"an":[116],"sequence":[120],"likelihood.":[121],"TERA":[122,147,171],"explores":[123],"reconciled":[125],"trees":[127],"that":[128,146,186],"can":[129],"be":[130],"amalgamated":[131],"from":[132,180,221],"sample":[134],"trees.":[137],"Using":[138],"large":[140],"scale":[141],"simulated":[142],"dataset,":[143],"demonstrate":[145],"achieves":[148],"same":[150],"accuracy":[151,167],"as":[152],"corresponding":[154],"while":[157],"being":[158],"faster,":[159],"outperforms":[161],"other":[162],"parsimony-based":[163],"both":[166],"speed.":[169],"Running":[170],"set":[174],"1099":[176],"homologous":[177],"families":[179],"complete":[181],"cyanobacterial":[182],"genomes,":[183],"find":[185],"incorporating":[187],"knowledge":[188],"results":[193],"two":[196],"thirds":[197],"reduction":[198],"number":[201],"apparent":[203],"events.":[205],"Availability":[206],"implementation:":[208],"The":[209],"algorithm":[210],"is":[211,218],"implemented":[212],"our":[214],"program":[215],"TERA,":[216],"which":[217],"freely":[219],"available":[220,231],"http://mbb.univ-montp2.fr/MBB/download_sources/16__TERA.":[222],"Contact:":[223],"celine.scornavacca@univ-montp2.fr,":[224],"ssolo@angel.elte.hu":[225],"Supplementary":[226,228],"information:":[227],"data":[229],"at":[232],"Bioinformatics":[233],"online.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":9}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
