{"id":"https://openalex.org/W2118058771","doi":"https://doi.org/10.1186/1748-7188-6-7","title":"An experimental study of Quartets MaxCut and other supertree methods","display_name":"An experimental study of Quartets MaxCut and other supertree methods","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W2118058771","doi":"https://doi.org/10.1186/1748-7188-6-7","mag":"2118058771","pmid":"https://pubmed.ncbi.nlm.nih.gov/21504600"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-6-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-6-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109080904","display_name":"M. Shel Swenson","orcid":null},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M Shel Swenson","raw_affiliation_strings":["Department of Computer Science, The University of Texas at Austin, Austin TX, USA. mswenson@cs.utexas.edu","Dept. of Computer Science, The University of Texas at Austin, Austin, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Texas at Austin, Austin TX, USA. mswenson@cs.utexas.edu","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Dept. of Computer Science, The University of Texas at Austin, Austin, USA#TAB#","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062049373","display_name":"Rahul Suri","orcid":null},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rahul Suri","raw_affiliation_strings":["Department of Computer Science, The University of Texas at Austin, Austin, TX,, USA","Dept. of Computer Science, The University of Texas at Austin, Austin, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Texas at Austin, Austin, TX,, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Dept. of Computer Science, The University of Texas at Austin, Austin, USA#TAB#","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026339571","display_name":"C. Randal Linder","orcid":null},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C Randal Linder","raw_affiliation_strings":["Section of Integrative Biology, The University of Texas at Austin, Austin, TX, USA","Section of Integrative Biology, The University of Texas at Austin, Austin, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Integrative Biology, The University of Texas at Austin, Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Section of Integrative Biology, The University of Texas at Austin, Austin, USA","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032411541","display_name":"Tandy Warnow","orcid":"https://orcid.org/0000-0001-7717-3514"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tandy Warnow","raw_affiliation_strings":["Department of Computer Science, The University of Texas at Austin, Austin, TX,, USA","Dept. of Computer Science, The University of Texas at Austin, Austin, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Texas at Austin, Austin, TX,, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Dept. of Computer Science, The University of Texas at Austin, Austin, USA#TAB#","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5109080904"],"corresponding_institution_ids":["https://openalex.org/I86519309"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":2.3094,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.88799657,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"6","issue":"1","first_page":"7","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7146000266075134,"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":0.7146000266075134,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0284000001847744,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.02449999935925007,"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/supertree","display_name":"Supertree","score":0.9954470992088318},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6108303070068359},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5586077570915222},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5577093362808228},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4190003275871277},{"id":"https://openalex.org/keywords/limit","display_name":"Limit (mathematics)","score":0.4153459668159485},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37421277165412903},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.3509412705898285},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33668625354766846},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.3283180594444275},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2980346977710724},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.1599113643169403},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14809352159500122}],"concepts":[{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.9954470992088318},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6108303070068359},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5586077570915222},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5577093362808228},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4190003275871277},{"id":"https://openalex.org/C151201525","wikidata":"https://www.wikidata.org/wiki/Q177239","display_name":"Limit (mathematics)","level":2,"score":0.4153459668159485},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37421277165412903},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.3509412705898285},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33668625354766846},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3283180594444275},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2980346977710724},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.1599113643169403},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14809352159500122},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1748-7188-6-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-6-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:21504600","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21504600","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3101644","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3101644","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":"Algorithms Mol Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:bde227e6f74546cd8a3ae47dac19028d","is_oa":true,"landing_page_url":"https://doaj.org/article/bde227e6f74546cd8a3ae47dac19028d","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 6, Iss 1, p 7 (2011)","raw_type":"article"},{"id":"pmh:oai:repositories.lib.utexas.edu:2152/27804","is_oa":true,"landing_page_url":"http://hdl.handle.net/2152/27804","pdf_url":null,"source":{"id":"https://openalex.org/S4306400568","display_name":"Texas ScholarWorks (Texas Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210102904","host_organization_name":"Texas Digital Library","host_organization_lineage":["https://openalex.org/I4210102904"],"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":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-6-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-6-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/1","display_name":"No poverty"}],"awards":[{"id":"https://openalex.org/G284709842","display_name":"IGERT:  Computational Phylogenetics and Applications to Biology","funder_award_id":"0114387","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6498455202","display_name":"Information Technology Research (ITR):   Building the Tree of Life -- A National Resource for Phyloinformatics and Computational Phylogenetics","funder_award_id":"0331453","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6729404461","display_name":"Collaborative Research: Large-scale simultaneous multiple alignment and phylogeny estimation","funder_award_id":"0733029","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2118058771.pdf","grobid_xml":"https://content.openalex.org/works/W2118058771.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1596422325","https://openalex.org/W1834136713","https://openalex.org/W1969378935","https://openalex.org/W1981037505","https://openalex.org/W1992800126","https://openalex.org/W1995615099","https://openalex.org/W2000387721","https://openalex.org/W2038370559","https://openalex.org/W2048878652","https://openalex.org/W2076210581","https://openalex.org/W2083213362","https://openalex.org/W2094277888","https://openalex.org/W2099272153","https://openalex.org/W2107471052","https://openalex.org/W2115318249","https://openalex.org/W2126763909","https://openalex.org/W2134766004","https://openalex.org/W2136538032","https://openalex.org/W2137384236","https://openalex.org/W2148317584","https://openalex.org/W2152113565","https://openalex.org/W2162725264","https://openalex.org/W2164997158","https://openalex.org/W2168696662","https://openalex.org/W2315781448","https://openalex.org/W2579372702","https://openalex.org/W3162014451","https://openalex.org/W4236627017","https://openalex.org/W4239241702","https://openalex.org/W4244179086","https://openalex.org/W4250164480"],"related_works":["https://openalex.org/W2145844324","https://openalex.org/W3111214985","https://openalex.org/W70956880","https://openalex.org/W4233205955","https://openalex.org/W2570931575","https://openalex.org/W2086288781","https://openalex.org/W2168234145","https://openalex.org/W2299622294","https://openalex.org/W4291200926","https://openalex.org/W2964156812"],"abstract_inverted_index":{"BACKGROUND:":[0],"Supertree":[1],"methods":[2,43,61,69,81,148,160,204,241],"represent":[3],"one":[4],"of":[5,13,40,51,59,108,124,130,180,209,239],"the":[6,11,30,38,46,79,109,120,126,131,134,181,207,228],"major":[7],"ways":[8],"by":[9],"which":[10],"Tree":[12],"Life":[14],"can":[15],"be":[16,172],"estimated,":[17],"but":[18],"despite":[19],"many":[20,74],"recent":[21],"algorithmic":[22,32],"innovations,":[23],"matrix":[24],"representation":[25],"with":[26,102,141,227],"parsimony":[27],"(MRP)":[28],"remains":[29],"main":[31],"supertree":[33,42,68,100,132,142,147,159,184,203,216,220,240],"method.":[34],"RESULTS:":[35],"We":[36,93],"evaluated":[37],"performance":[39],"several":[41],"based":[44],"upon":[45,163,191],"Quartets":[47],"MaxCut":[48],"(QMC)":[49],"method":[50],"Snir":[52],"and":[53,55,65,167,177,237],"Rao":[54],"showed":[56,118],"that":[57,70,85,96,119,158,161,168],"two":[58],"these":[60],"usually":[62],"outperform":[63],"MRP":[64,164],"five":[66],"other":[67],"we":[71,117],"studied,":[72],"under":[73],"realistic":[75],"model":[76],"conditions.":[77],"However,":[78],"QMC-based":[80],"have":[82],"scalability":[83],"issues":[84],"may":[86],"limit":[87],"their":[88],"utility":[89],"on":[90,149],"large":[91,199],"datasets.":[92],"also":[94],"observed":[95],"taxon":[97,192],"sampling":[98,193],"impacted":[99],"accuracy,":[101],"poor":[103],"results":[104,156],"obtained":[105],"when":[106],"all":[107],"source":[110,135,210,234],"trees":[111,136,201],"were":[112],"only":[113,138,224],"sparsely":[114],"sampled.":[115],"Finally,":[116,218],"popular":[121],"optimality":[122],"criterion":[123],"minimizing":[125],"total":[127],"topological":[128,143,188,221,230],"distance":[129,231],"to":[133,174,196,232],"is":[137,152,223],"weakly":[139,225],"correlated":[140,226],"accuracy.":[144],"Therefore":[145],"evaluating":[146],"biological":[150],"datasets":[151],"problematic.":[153],"CONCLUSIONS:":[154],"Our":[155],"show":[157],"improve":[162],"are":[165],"possible,":[166],"an":[169],"effort":[170],"should":[171,205],"made":[173],"produce":[175],"scalable":[176],"robust":[178],"implementations":[179],"most":[182],"accurate":[183],"methods.":[185,217],"Also,":[186],"because":[187],"accuracy":[189],"depends":[190],"strategies,":[194],"attempts":[195],"construct":[197],"very":[198],"phylogenetic":[200],"using":[202],"consider":[206],"selection":[208],"tree":[211],"datasets,":[212],"as":[213,215],"well":[214],"since":[219],"error":[222],"supertree's":[229],"its":[233],"trees,":[235],"development":[236],"testing":[238],"presents":[242],"methodological":[243],"challenges.":[244]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}