{"id":"https://openalex.org/W3138529574","doi":"https://doi.org/10.1093/bioinformatics/btac326","title":"Building alternative consensus trees and supertrees using <i>k</i> -means and Robinson and Foulds distance","display_name":"Building alternative consensus trees and supertrees using <i>k</i> -means and Robinson and Foulds distance","publication_year":2022,"publication_date":"2022-05-10","ids":{"openalex":"https://openalex.org/W3138529574","doi":"https://doi.org/10.1093/bioinformatics/btac326","mag":"3138529574","pmid":"https://pubmed.ncbi.nlm.nih.gov/35579343"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac326","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac326","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083583971","display_name":"Nadia Tahiri","orcid":"https://orcid.org/0000-0002-1818-208X"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]},{"id":"https://openalex.org/I159129438","display_name":"Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al","ror":"https://ror.org/002rjbv21","country_code":"CA","type":"education","lineage":["https://openalex.org/I159129438","https://openalex.org/I49663120"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nadia Tahiri","raw_affiliation_strings":["D\u00e9partement d\u2019informatique, Universit\u00e9 de Sherbrooke , Sherbrooke, QC J1K 2X9, Canada","D\u00e9partement d\u2019informatique, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montreal, QC H2X 3Y7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement d\u2019informatique, Universit\u00e9 de Sherbrooke , Sherbrooke, QC J1K 2X9, Canada","institution_ids":["https://openalex.org/I135117807"]},{"raw_affiliation_string":"D\u00e9partement d\u2019informatique, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montreal, QC H2X 3Y7, Canada","institution_ids":["https://openalex.org/I159129438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082996278","display_name":"Bernard Fichet","orcid":null},"institutions":[{"id":"https://openalex.org/I21491767","display_name":"Aix-Marseille Universit\u00e9","ror":"https://ror.org/035xkbk20","country_code":"FR","type":"education","lineage":["https://openalex.org/I21491767"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Bernard Fichet","raw_affiliation_strings":["Facult\u00e9 de M\u00e9decine, Aix-Marseille Universit\u00e9 , Marseille F-13385, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Facult\u00e9 de M\u00e9decine, Aix-Marseille Universit\u00e9 , Marseille F-13385, France","institution_ids":["https://openalex.org/I21491767"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004592090","display_name":"Vladimir Makarenkov","orcid":"https://orcid.org/0000-0003-3753-5925"},"institutions":[{"id":"https://openalex.org/I159129438","display_name":"Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al","ror":"https://ror.org/002rjbv21","country_code":"CA","type":"education","lineage":["https://openalex.org/I159129438","https://openalex.org/I49663120"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Vladimir Makarenkov","raw_affiliation_strings":["D\u00e9partement d\u2019informatique, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montreal, QC H2X 3Y7, Canada"],"raw_orcid":"https://orcid.org/0000-0003-3753-5925","affiliations":[{"raw_affiliation_string":"D\u00e9partement d\u2019informatique, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montreal, QC H2X 3Y7, Canada","institution_ids":["https://openalex.org/I159129438"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5004592090"],"corresponding_institution_ids":["https://openalex.org/I159129438"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.693,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.65435877,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"38","issue":"13","first_page":"3367","last_page":"3376"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.44449999928474426,"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":0.44449999928474426,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1655000001192093,"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/T10637","display_name":"Advanced Clustering Algorithms Research","score":0.07729999721050262,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5629767775535583}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5629767775535583}],"mesh":[{"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":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac326","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac326","pdf_url":null,"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:35579343","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35579343","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}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":88,"referenced_works":["https://openalex.org/W171996032","https://openalex.org/W191887720","https://openalex.org/W248218665","https://openalex.org/W1498782169","https://openalex.org/W1586146320","https://openalex.org/W1589227310","https://openalex.org/W1596422325","https://openalex.org/W1774207464","https://openalex.org/W1867732144","https://openalex.org/W1963957860","https://openalex.org/W1965612692","https://openalex.org/W1971158963","https://openalex.org/W1977358834","https://openalex.org/W1978384785","https://openalex.org/W1981037505","https://openalex.org/W1982901388","https://openalex.org/W1987971958","https://openalex.org/W1992800126","https://openalex.org/W1993371508","https://openalex.org/W2000034617","https://openalex.org/W2001076853","https://openalex.org/W2002586964","https://openalex.org/W2003064123","https://openalex.org/W2004798786","https://openalex.org/W2010140249","https://openalex.org/W2012949957","https://openalex.org/W2019182846","https://openalex.org/W2047715328","https://openalex.org/W2055298722","https://openalex.org/W2060425093","https://openalex.org/W2070620318","https://openalex.org/W2071949631","https://openalex.org/W2078969200","https://openalex.org/W2082246635","https://openalex.org/W2085487226","https://openalex.org/W2092339835","https://openalex.org/W2094277888","https://openalex.org/W2099272153","https://openalex.org/W2103718624","https://openalex.org/W2103849916","https://openalex.org/W2105580430","https://openalex.org/W2107387420","https://openalex.org/W2108435369","https://openalex.org/W2109014721","https://openalex.org/W2112620675","https://openalex.org/W2115137014","https://openalex.org/W2122451634","https://openalex.org/W2124808846","https://openalex.org/W2127218421","https://openalex.org/W2128950382","https://openalex.org/W2129696562","https://openalex.org/W2132762477","https://openalex.org/W2132926880","https://openalex.org/W2134415959","https://openalex.org/W2143277118","https://openalex.org/W2143794041","https://openalex.org/W2145769273","https://openalex.org/W2150593711","https://openalex.org/W2154675536","https://openalex.org/W2159813603","https://openalex.org/W2160517437","https://openalex.org/W2163949171","https://openalex.org/W2168696662","https://openalex.org/W2170587743","https://openalex.org/W2211675957","https://openalex.org/W2308528431","https://openalex.org/W2315781448","https://openalex.org/W2496112388","https://openalex.org/W2605343262","https://openalex.org/W2732829080","https://openalex.org/W2799524357","https://openalex.org/W2805555771","https://openalex.org/W2962924242","https://openalex.org/W3009784754","https://openalex.org/W3013152614","https://openalex.org/W3031411888","https://openalex.org/W3046218112","https://openalex.org/W3098329170","https://openalex.org/W3107032386","https://openalex.org/W3125550983","https://openalex.org/W3138967247","https://openalex.org/W4210681352","https://openalex.org/W4233325831","https://openalex.org/W4250164480","https://openalex.org/W6635013723","https://openalex.org/W6639077426","https://openalex.org/W6676358527","https://openalex.org/W6786673101"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"Each":[1],"gene":[2,31,42,116],"has":[3],"its":[4,47,238],"own":[5,48],"evolutionary":[6,13,38,55,109,228],"history":[7,39],"which":[8,51],"can":[9,25,141],"substantially":[10],"differ":[11],"from":[12,57],"histories":[14],"of":[15,40,67,73,111,115,124,135,149,162,195,201,205,209],"other":[16],"genes.":[17],"For":[18],"example,":[19],"some":[20,132],"individual":[21],"genes":[22],"or":[23,33,77,86,156],"operons":[24],"be":[26,44,142],"affected":[27],"by":[28,46],"specific":[29],"horizontal":[30],"transfer":[32],"recombination":[34],"events.":[35],"Thus,":[36],"the":[37,58,64,71,106,125,136,167,189,202,206,210,216],"each":[41],"should":[43],"represented":[45],"phylogenetic":[49],"tree":[50,60,76,85,180,218],"may":[52],"display":[53],"different":[54],"patterns":[56,66,110],"species":[59],"that":[61],"accounts":[62],"for":[63,95,225],"main":[65],"vertical":[68],"descent.":[69],"However,":[70],"output":[72],"traditional":[74],"consensus":[75,84,99],"supertree":[78],"inference":[79],"methods":[80],"is":[81,186,242],"a":[82,91,112,146],"unique":[83],"supertree.":[87],"RESULTS:":[88],"We":[89,118],"present":[90],"new":[92],"efficient":[93],"method":[94,211],"inferring":[96,196],"multiple":[97,157],"alternative":[98,197],"trees":[100,150],"and":[101,138,172,174,221],"supertrees":[102],"to":[103,144,179,188],"best":[104],"represent":[105],"most":[107],"important":[108],"given":[113,147,187],"set":[114,148],"phylogenies.":[117],"show":[119],"how":[120],"an":[121],"adapted":[122],"version":[123],"popular":[126,168],"k-means":[127],"clustering":[128,181,219],"algorithm,":[129],"based":[130],"on":[131],"remarkable":[133],"properties":[134],"Robinson":[137],"Foulds":[139],"distance,":[140],"used":[143],"partition":[145],"into":[151],"one":[152],"(for":[153,158],"homogeneous":[154],"data)":[155,160],"heterogeneous":[159],"cluster(s)":[161],"trees.":[163],"Moreover,":[164],"we":[165],"adapt":[166],"Cali\u0144ski-Harabasz,":[169],"Silhouette,":[170],"Ball":[171],"Hall,":[173],"Gap":[175],"cluster":[176],"validity":[177],"indices":[178],"with":[182,237],"k-means.":[183],"Special":[184],"attention":[185],"relevant":[190],"but":[191],"very":[192],"challenging":[193],"problem":[194],"supertrees.":[198],"The":[199],"use":[200],"Euclidean":[203],"property":[204],"objective":[207],"function":[208],"makes":[212],"it":[213],"faster":[214],"than":[215],"existing":[217],"techniques,":[220],"thus":[222],"better":[223],"suited":[224],"analyzing":[226],"large":[227],"datasets.":[229],"AVAILABILITY":[230],"AND":[231],"IMPLEMENTATION:":[232],"Our":[233],"KMeansSuperTreeClustering":[234],"program":[235],"along":[236],"C++":[239],"source":[240],"code":[241],"available":[243,251],"at:":[244],"https://github.com/TahiriNadia/KMeansSuperTreeClustering.":[245],"SUPPLEMENTARY":[246],"INFORMATION:":[247],"Supplementary":[248],"data":[249],"are":[250],"at":[252],"Bioinformatics":[253],"online.":[254]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2021-03-29T00:00:00"}
