{"id":"https://openalex.org/W3164715403","doi":"https://doi.org/10.1093/bioinformatics/btab428","title":"wQFM: highly accurate genome-scale species tree estimation from weighted quartets","display_name":"wQFM: highly accurate genome-scale species tree estimation from weighted quartets","publication_year":2021,"publication_date":"2021-06-03","ids":{"openalex":"https://openalex.org/W3164715403","doi":"https://doi.org/10.1093/bioinformatics/btab428","mag":"3164715403"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab428","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab428","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"],"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/A5049610333","display_name":"M. Mahbub","orcid":"https://orcid.org/0000-0002-1343-7493"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Mahim Mahbub","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067730186","display_name":"Zahin Wahab","orcid":null},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Zahin Wahab","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058195213","display_name":"Rezwana Reaz","orcid":"https://orcid.org/0000-0002-6809-9516"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":true,"raw_author_name":"Rezwana Reaz","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100733249","display_name":"Mohammad Saifur Rahman","orcid":"https://orcid.org/0000-0002-9887-4456"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"M Saifur Rahman","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063693993","display_name":"Md. Shamsuzzoha Bayzid","orcid":"https://orcid.org/0000-0002-5640-0615"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":true,"raw_author_name":"Md Shamsuzzoha Bayzid","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5058195213","https://openalex.org/A5063693993"],"corresponding_institution_ids":["https://openalex.org/I183697816"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4395,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.90096504,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"37","issue":"21","first_page":"3734","last_page":"3743"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9987000226974487,"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/T14049","display_name":"Plant and Fungal Species Descriptions","score":0.9901000261306763,"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/coalescent-theory","display_name":"Coalescent theory","score":0.9459829926490784},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6888270378112793},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.527980387210846},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5244631767272949},{"id":"https://openalex.org/keywords/locus","display_name":"Locus (genetics)","score":0.47172942757606506},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4346328377723694},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41196635365486145},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40848231315612793},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35947921872138977},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32623642683029175},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26490193605422974},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2176057994365692},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16435164213180542},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10159263014793396}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.9459829926490784},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6888270378112793},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.527980387210846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5244631767272949},{"id":"https://openalex.org/C84597430","wikidata":"https://www.wikidata.org/wiki/Q106227","display_name":"Locus (genetics)","level":3,"score":0.47172942757606506},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4346328377723694},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41196635365486145},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40848231315612793},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35947921872138977},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32623642683029175},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26490193605422974},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2176057994365692},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16435164213180542},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10159263014793396}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btab428","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab428","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"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6700000166893005,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F261270187","display_name":"Information and Communication Technology Division","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":87,"referenced_works":["https://openalex.org/W160062981","https://openalex.org/W1491635865","https://openalex.org/W1887892324","https://openalex.org/W1889423108","https://openalex.org/W1924404512","https://openalex.org/W1968830099","https://openalex.org/W1972157500","https://openalex.org/W1972805029","https://openalex.org/W1975933692","https://openalex.org/W1978199447","https://openalex.org/W1983753237","https://openalex.org/W1992732214","https://openalex.org/W1995615099","https://openalex.org/W1999083683","https://openalex.org/W2001418464","https://openalex.org/W2005937606","https://openalex.org/W2016171324","https://openalex.org/W2037654474","https://openalex.org/W2037749900","https://openalex.org/W2046132104","https://openalex.org/W2052432722","https://openalex.org/W2054652527","https://openalex.org/W2060425093","https://openalex.org/W2075503802","https://openalex.org/W2083015817","https://openalex.org/W2099272153","https://openalex.org/W2106704226","https://openalex.org/W2107555182","https://openalex.org/W2107608009","https://openalex.org/W2108039804","https://openalex.org/W2108116104","https://openalex.org/W2114227052","https://openalex.org/W2114430361","https://openalex.org/W2119837484","https://openalex.org/W2120323779","https://openalex.org/W2120663060","https://openalex.org/W2123800174","https://openalex.org/W2124511083","https://openalex.org/W2125024684","https://openalex.org/W2125129601","https://openalex.org/W2127713506","https://openalex.org/W2130353415","https://openalex.org/W2131551905","https://openalex.org/W2132714045","https://openalex.org/W2137180017","https://openalex.org/W2139050004","https://openalex.org/W2140122507","https://openalex.org/W2141835782","https://openalex.org/W2145562754","https://openalex.org/W2145608399","https://openalex.org/W2148012025","https://openalex.org/W2148723086","https://openalex.org/W2151320514","https://openalex.org/W2152113565","https://openalex.org/W2155132113","https://openalex.org/W2157127204","https://openalex.org/W2158482855","https://openalex.org/W2160936843","https://openalex.org/W2162336040","https://openalex.org/W2164997158","https://openalex.org/W2165045652","https://openalex.org/W2170996473","https://openalex.org/W2174889714","https://openalex.org/W2177324599","https://openalex.org/W2178890195","https://openalex.org/W2179623716","https://openalex.org/W2277574918","https://openalex.org/W2323303653","https://openalex.org/W2472554530","https://openalex.org/W2500162386","https://openalex.org/W2504969600","https://openalex.org/W2579181634","https://openalex.org/W2594449772","https://openalex.org/W2601425645","https://openalex.org/W2801361050","https://openalex.org/W2896179295","https://openalex.org/W2910289366","https://openalex.org/W2952624837","https://openalex.org/W2975887780","https://openalex.org/W3004334340","https://openalex.org/W3012620190","https://openalex.org/W3019023988","https://openalex.org/W3049597178","https://openalex.org/W3102172121","https://openalex.org/W3141994502","https://openalex.org/W4210633230","https://openalex.org/W4231969088"],"related_works":["https://openalex.org/W2952954362","https://openalex.org/W3093602888","https://openalex.org/W3156045358","https://openalex.org/W2921578049","https://openalex.org/W2581424563","https://openalex.org/W2020599444","https://openalex.org/W2362218761","https://openalex.org/W2062354928","https://openalex.org/W2113708670","https://openalex.org/W2088120817"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Species":[2],"tree":[3,20,102,130,203],"estimation":[4,131,204],"from":[5,8,57,132],"genes":[6],"sampled":[7],"throughout":[9],"the":[10,17,29,85,93,137,159,167,180,195,215],"whole":[11],"genome":[12],"is":[13,26,118,164,179,192],"complicated":[14],"due":[15,66],"to":[16,67,84,96,142,171],"gene":[18,61],"tree\u2013species":[19],"discordance.":[21],"Incomplete":[22],"lineage":[23],"sorting":[24],"(ILS)":[25],"one":[27,165,193],"of":[28,60,88,110,152,166,194,217],"most":[30,196],"frequent":[31],"causes":[32],"for":[33,42,53,105,128,184],"this":[34,227],"discordance,":[35],"where":[36,81],"alleles":[37],"can":[38,103],"coexist":[39],"in":[40,226],"populations":[41],"periods":[43],"that":[44,209],"may":[45],"span":[46],"several":[47],"speciation":[48],"events.":[49],"Quartet-based":[50],"summary":[51],"methods":[52],"estimating":[54,111],"species":[55,101,112,129,202],"trees":[56,62],"a":[58,98,106,124,143,150],"collection":[59,151],"are":[63,234,242],"becoming":[64],"popular":[65],"their":[68],"high":[69],"accuracy":[70,216],"and":[71,90,154,188,198,219,222,229],"statistical":[72],"guarantee":[73],"under":[74],"ILS.":[75],"Generating":[76],"quartets":[77,95,117],"with":[78,176,189],"appropriate":[79],"weights,":[80],"weights":[82],"correspond":[83],"relative":[86],"importance":[87],"quartets,":[89],"subsequently":[91],"amalgamating":[92],"weighted":[94,116,144,185],"infer":[97],"single":[99],"coherent":[100],"allow":[104],"statistically":[107],"consistent":[108],"way":[109],"trees.":[113],"However,":[114],"handling":[115],"challenging.":[119],"Results":[120],"We":[121,173],"propose":[122],"wQFM,":[123],"highly":[125],"accurate":[126,197],"method":[127,183],"multi-locus":[133],"data,":[134],"by":[135],"extending":[136],"quartet":[138,186],"FM":[139],"(QFM)":[140],"algorithm":[141],"setting.":[145],"wQFM":[146,175,210,230],"was":[147],"assessed":[148],"on":[149],"simulated":[153],"real":[155],"biological":[156],"datasets,":[157],"including":[158],"avian":[160],"phylogenomic":[161,169],"dataset,":[162],"which":[163,178,191],"largest":[168],"datasets":[170],"date.":[172],"compared":[174],"wQMC,":[177],"best":[181],"alternate":[182],"amalgamation,":[187],"ASTRAL,":[190],"widely":[199],"used":[200],"coalescent-based":[201],"methods.":[205],"Our":[206],"results":[207],"suggest":[208],"matches":[211],"or":[212],"improves":[213],"upon":[214],"wQMC":[218],"ASTRAL.":[220],"Availability":[221],"implementation":[223],"Datasets":[224],"studied":[225],"article":[228],"(in":[231],"open-source":[232],"form)":[233],"available":[235,243],"at":[236,244],"https://github.com/Mahim1997/wQFM-2020.":[237],"Supplementary":[238,240],"information":[239],"data":[241],"Bioinformatics":[245],"online.":[246]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2021-06-07T00:00:00"}
