{"id":"https://openalex.org/W2165228561","doi":"https://doi.org/10.1186/1471-2105-9-413","title":"PhySIC_IST: cleaning source trees to infer more informative supertrees","display_name":"PhySIC_IST: cleaning source trees to infer more informative supertrees","publication_year":2008,"publication_date":"2008-10-04","ids":{"openalex":"https://openalex.org/W2165228561","doi":"https://doi.org/10.1186/1471-2105-9-413","mag":"2165228561","pmid":"https://pubmed.ncbi.nlm.nih.gov/18834542"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-413","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-413","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-413","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-413","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/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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Celine Scornavacca","raw_affiliation_strings":["Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Universit\u00e9 Montpellier II, Place E, Bataillon - CC 064 - 34095 Montpellier Cedex 5, France. scornava@lirmm.fr","Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Universit\u00e9 Montpellier II, Place E. Bataillon \u2013 CC 064, 34095, Montpellier Cedex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Universit\u00e9 Montpellier II, Place E, Bataillon - CC 064 - 34095 Montpellier Cedex 5, France. scornava@lirmm.fr","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210105943"]},{"raw_affiliation_string":"Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Universit\u00e9 Montpellier II, Place E. Bataillon \u2013 CC 064, 34095, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210105943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058327913","display_name":"Vincent Berry","orcid":"https://orcid.org/0000-0001-7271-4027"},"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":true,"raw_author_name":"Vincent Berry","raw_affiliation_strings":["Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier (LIRMM, UMR 5506, CNRS), Universit\u00e9 Montpellier II 161, rue Ada, 34392, Montpellier Cedex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier (LIRMM, UMR 5506, CNRS), Universit\u00e9 Montpellier II 161, rue Ada, 34392, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210101743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088743342","display_name":"Vincent Lefort","orcid":"https://orcid.org/0000-0003-2864-4783"},"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":"Vincent Lefort","raw_affiliation_strings":["Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier (LIRMM, UMR 5506, CNRS), Universit\u00e9 Montpellier II 161, rue Ada, 34392, Montpellier Cedex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier (LIRMM, UMR 5506, CNRS), Universit\u00e9 Montpellier II 161, rue Ada, 34392, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210101743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023646775","display_name":"Emmanuel Douzery","orcid":"https://orcid.org/0000-0001-5286-647X"},"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/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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Emmanuel JP Douzery","raw_affiliation_strings":["Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Universit\u00e9 Montpellier II, Place E. Bataillon \u2013 CC 064, 34095, Montpellier Cedex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Universit\u00e9 Montpellier II, Place E. Bataillon \u2013 CC 064, 34095, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210105943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025043496","display_name":"Vincent Ranwez","orcid":"https://orcid.org/0000-0002-9308-7541"},"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/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"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Vincent Ranwez","raw_affiliation_strings":["Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Universit\u00e9 Montpellier II, Place E. Bataillon \u2013 CC 064, 34095, Montpellier Cedex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Universit\u00e9 Montpellier II, Place E. Bataillon \u2013 CC 064, 34095, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210105943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025043496","https://openalex.org/A5058327913"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210105943"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.5601,"has_fulltext":true,"cited_by_count":55,"citation_normalized_percentile":{"value":0.82527951,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"413","last_page":"413"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9345999956130981,"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":0.9345999956130981,"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/T10895","display_name":"Species Distribution and Climate Change","score":0.010400000028312206,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.004999999888241291,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/supertree","display_name":"Supertree","score":0.9484116435050964},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5593782067298889},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5450480580329895},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.504644513130188},{"id":"https://openalex.org/keywords/taxon","display_name":"Taxon","score":0.4819785952568054},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4491087794303894},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44456571340560913},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.4258440136909485},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.41825318336486816},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3832945227622986},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3815653920173645},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.3618806004524231},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32721972465515137},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29259157180786133},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.26470327377319336},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2142585813999176},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20252037048339844},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.13691949844360352},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13075605034828186},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.11072570085525513}],"concepts":[{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.9484116435050964},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5593782067298889},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5450480580329895},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.504644513130188},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.4819785952568054},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4491087794303894},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44456571340560913},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.4258440136909485},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.41825318336486816},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3832945227622986},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3815653920173645},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.3618806004524231},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32721972465515137},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29259157180786133},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.26470327377319336},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2142585813999176},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20252037048339844},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.13691949844360352},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13075605034828186},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.11072570085525513}],"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":"D001699","descriptor_name":"Biometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003663","descriptor_name":"Decision Trees","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003663","descriptor_name":"Decision Trees","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003663","descriptor_name":"Decision Trees","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-9-413","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-413","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-413","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18834542","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18834542","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2576265","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2576265","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:HAL:lirmm-00324069v1","is_oa":false,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-00324069","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":"http://www.atgc-montpellier.fr/physic ist/","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:fa1ed70ac4e8427b822c2349ffe87847","is_oa":false,"landing_page_url":"https://doaj.org/article/fa1ed70ac4e8427b822c2349ffe87847","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 413 (2008)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-413","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-413","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-413","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2165228561.pdf","grobid_xml":"https://content.openalex.org/works/W2165228561.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W62347558","https://openalex.org/W1523496868","https://openalex.org/W1563401818","https://openalex.org/W1569184144","https://openalex.org/W1596422325","https://openalex.org/W1633681515","https://openalex.org/W1834136713","https://openalex.org/W1884098403","https://openalex.org/W2033854905","https://openalex.org/W2036164339","https://openalex.org/W2038848746","https://openalex.org/W2040811618","https://openalex.org/W2041797002","https://openalex.org/W2055764798","https://openalex.org/W2065461553","https://openalex.org/W2065746563","https://openalex.org/W2078109763","https://openalex.org/W2087009076","https://openalex.org/W2088120817","https://openalex.org/W2096641211","https://openalex.org/W2096977241","https://openalex.org/W2100361188","https://openalex.org/W2103546861","https://openalex.org/W2106706740","https://openalex.org/W2115031948","https://openalex.org/W2115318249","https://openalex.org/W2121052765","https://openalex.org/W2125087754","https://openalex.org/W2132080607","https://openalex.org/W2135157209","https://openalex.org/W2151690408","https://openalex.org/W2158878884","https://openalex.org/W2171189056","https://openalex.org/W2184489641","https://openalex.org/W2477279521","https://openalex.org/W2982761114","https://openalex.org/W3015805353","https://openalex.org/W3217097258","https://openalex.org/W4205112646","https://openalex.org/W4244179086","https://openalex.org/W4285719527","https://openalex.org/W4301464301"],"related_works":["https://openalex.org/W1505289225","https://openalex.org/W648879837","https://openalex.org/W2150133233","https://openalex.org/W2474028989","https://openalex.org/W2109031698","https://openalex.org/W2036812417","https://openalex.org/W4389726854","https://openalex.org/W2057191541","https://openalex.org/W2145527356","https://openalex.org/W3009510969"],"abstract_inverted_index":{"BACKGROUND:":[0],"Supertree":[1],"methods":[2,48,58,89,361],"combine":[3],"phylogenies":[4],"with":[5,171,252,258,325],"overlapping":[6],"sets":[7],"of":[8,79,90,146,184,192,206,211,245,359],"taxa":[9,120],"into":[10,201],"a":[11,76,84,144,185,190,217,238,259,273],"larger":[12],"one.":[13],"Topological":[14],"conflicts":[15,42,81],"frequently":[16],"arise":[17],"among":[18,44,132],"source":[19,45,64,73,124,133,229,247,254,317,355],"trees":[20,74,134,230,318],"for":[21,136],"methodological":[22],"or":[23,36,82,135],"biological":[24,302],"reasons,":[25],"such":[26],"as":[27,170,175,177,350,352],"long":[28],"branch":[29],"attraction,":[30],"lateral":[31],"gene":[32,34,38],"transfers,":[33],"duplication/loss":[35],"deep":[37],"coalescence.":[39],"When":[40,71],"topological":[41,80],"occur":[43],"trees,":[46,125],"liberal":[47,239,269],"infer":[49,59,108,155],"supertrees":[50,60,112,162,286,323,349],"containing":[51],"the":[52,72,119,123,147,165,193,204,209,228,233,243,297,309,316,344,354,360],"most":[53],"frequent":[54],"alternative,":[55],"while":[56,173,289,319],"veto":[57,149,260,267],"not":[61,115],"contradicting":[62],"any":[63],"tree,":[65],"i.e.":[66,111],"discard":[67],"all":[68,118],"conflicting":[69],"resolutions.":[70],"host":[75],"significant":[77],"number":[78],"have":[83],"small":[85],"taxon":[86],"overlap,":[87],"supertree":[88,186,234],"both":[91,203],"kinds":[92],"can":[93,154],"propose":[94,106,216],"poorly":[95],"resolved,":[96],"hence":[97],"uninformative,":[98],"supertrees.":[99,157],"RESULTS:":[100],"To":[101],"overcome":[102],"this":[103,180],"problem,":[104],"we":[105,215,278],"to":[107,226,232,296],"non-plenary":[109,156,348],"supertrees,":[110],"that":[113,153,163,199,241,249,280,308,342],"do":[114],"necessarily":[116],"contain":[117],"present":[121],"in":[122,315,328,346],"discarding":[126],"those":[127],"whose":[128],"position":[129],"greatly":[130],"differs":[131],"which":[137],"insufficient":[138],"information":[139],"is":[140,187,237,362],"provided.":[141],"We":[142],"detail":[143],"variant":[145],"PhySIC":[148],"method":[150,261],"called":[151,221],"PhySIC_IST":[152,158,339],"aims":[159],"at":[160],"inferring":[161,347],"satisfy":[164],"same":[166],"appealing":[167],"theoretical":[168],"properties":[169],"PhySIC,":[172,288],"being":[174],"informative":[176,285],"possible":[178],"under":[179],"constraint.":[181],"The":[182,331],"informativeness":[183],"estimated":[188],"using":[189],"variation":[191],"CIC":[194],"(Cladistic":[195],"Information":[196],"Content)":[197],"criterion,":[198],"takes":[200],"account":[202],"presence":[205],"multifurcations":[207],"and":[208,268,334,340],"absence":[210],"some":[212],"taxa.":[213],"Additionally,":[214],"statistical":[218],"preprocessing":[219,353],"step":[220,240],"STC":[222,236,257,310],"(Source":[223],"Trees":[224],"Correction)":[225],"correct":[227],"prior":[231],"inference.":[235],"removes":[242],"parts":[244],"each":[246],"tree":[248],"significantly":[250],"conflict":[251],"other":[253],"trees.":[255,356],"Combining":[256],"allows":[262],"an":[263],"explicit":[264],"trade-off":[265],"between":[266],"approaches,":[270],"tuned":[271],"by":[272],"single":[274],"parameter.Performing":[275],"large-scale":[276],"simulations,":[277],"observe":[279],"STC+PhySIC_IST":[281,320],"infers":[282],"much":[283],"more":[284],"than":[287],"preserving":[290],"low":[291],"type":[292],"I":[293],"error":[294],"compared":[295],"well-known":[298],"MRP":[299],"method.":[300],"Two":[301],"case":[303],"studies":[304],"on":[305],"animals":[306],"confirm":[307],"preprocess":[311],"successfully":[312],"detects":[313],"anomalies":[314],"provides":[321],"well-resolved":[322],"agreeing":[324],"current":[326],"knowledge":[327],"systematics.":[329],"CONCLUSION:":[330],"paper":[332],"introduces":[333],"tests":[335],"two":[336],"new":[337],"methodologies,":[338],"STC,":[341],"demonstrate":[343],"interest":[345],"well":[351],"An":[357],"implementation":[358],"available":[363],"at:":[364],"http://www.atgc-montpellier.fr/physic_ist/.":[365]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":4}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
