{"id":"https://openalex.org/W3162593345","doi":"https://doi.org/10.3390/a14050148","title":"Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation","display_name":"Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation","publication_year":2021,"publication_date":"2021-05-07","ids":{"openalex":"https://openalex.org/W3162593345","doi":"https://doi.org/10.3390/a14050148","mag":"3162593345"},"language":"en","primary_location":{"id":"doi:10.3390/a14050148","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14050148","pdf_url":"https://www.mdpi.com/1999-4893/14/5/148/pdf?version=1620463506","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/14/5/148/pdf?version=1620463506","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069222630","display_name":"Minhyuk Park","orcid":"https://orcid.org/0000-0002-8676-7565"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Minhyuk Park","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014969856","display_name":"Paul Zaharias","orcid":"https://orcid.org/0000-0003-3550-2636"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Zaharias","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"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/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tandy Warnow","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032411541"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.8945,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.72605112,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"14","issue":"5","first_page":"148","last_page":"148"},"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":0.9983999729156494,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.989300012588501,"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/disjoint-sets","display_name":"Disjoint sets","score":0.7484418749809265},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.7178522944450378},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6258924007415771},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6013907790184021},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5913934707641602},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.45678389072418213},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.44726741313934326},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.41764116287231445},{"id":"https://openalex.org/keywords/locus","display_name":"Locus (genetics)","score":0.4113794267177582},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39636820554733276},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36892688274383545},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2812187671661377},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.24260863661766052},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1385631561279297},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13365915417671204},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10981497168540955}],"concepts":[{"id":"https://openalex.org/C45340560","wikidata":"https://www.wikidata.org/wiki/Q215382","display_name":"Disjoint sets","level":2,"score":0.7484418749809265},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.7178522944450378},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6258924007415771},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6013907790184021},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5913934707641602},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.45678389072418213},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.44726741313934326},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.41764116287231445},{"id":"https://openalex.org/C84597430","wikidata":"https://www.wikidata.org/wiki/Q106227","display_name":"Locus (genetics)","level":3,"score":0.4113794267177582},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39636820554733276},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36892688274383545},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2812187671661377},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.24260863661766052},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1385631561279297},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13365915417671204},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10981497168540955},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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":4,"locations":[{"id":"doi:10.3390/a14050148","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14050148","pdf_url":"https://www.mdpi.com/1999-4893/14/5/148/pdf?version=1620463506","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:8c8e0543bc5148869da17130501465b0","is_oa":true,"landing_page_url":"https://doaj.org/article/8c8e0543bc5148869da17130501465b0","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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, Vol 14, Iss 5, p 148 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1999-4893/14/5/148/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/a14050148","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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; Volume 14; Issue 5; Pages: 148","raw_type":"Text"},{"id":"pmh:oai:www.ideals.illinois.edu:2142/110713","is_oa":false,"landing_page_url":"http://hdl.handle.net/2142/110713","pdf_url":null,"source":{"id":"https://openalex.org/S4377196349","display_name":"IDEALS (University of Illinois Urbana-Champaign)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I157725225","host_organization_name":"University of Illinois Urbana-Champaign","host_organization_lineage":["https://openalex.org/I157725225"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis"}],"best_oa_location":{"id":"doi:10.3390/a14050148","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14050148","pdf_url":"https://www.mdpi.com/1999-4893/14/5/148/pdf?version=1620463506","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3750374216","display_name":null,"funder_award_id":"1458652","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/W3162593345.pdf","grobid_xml":"https://content.openalex.org/works/W3162593345.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1580609970","https://openalex.org/W1593676244","https://openalex.org/W2007668764","https://openalex.org/W2031611770","https://openalex.org/W2056251063","https://openalex.org/W2060425093","https://openalex.org/W2065461553","https://openalex.org/W2108911240","https://openalex.org/W2111211467","https://openalex.org/W2111647009","https://openalex.org/W2141052558","https://openalex.org/W2145608399","https://openalex.org/W2147461064","https://openalex.org/W2152179349","https://openalex.org/W2152529266","https://openalex.org/W2157552136","https://openalex.org/W2159638180","https://openalex.org/W2161973008","https://openalex.org/W2763307239","https://openalex.org/W2794335363","https://openalex.org/W2886801015","https://openalex.org/W2890213685","https://openalex.org/W2949367299","https://openalex.org/W2949867654","https://openalex.org/W2955099628","https://openalex.org/W2963132458","https://openalex.org/W3005235420","https://openalex.org/W3016794363","https://openalex.org/W3025962679","https://openalex.org/W3044581192","https://openalex.org/W3083304049","https://openalex.org/W3092664098","https://openalex.org/W3109134151","https://openalex.org/W3135191472","https://openalex.org/W3143110774","https://openalex.org/W6634604597"],"related_works":["https://openalex.org/W1971174658","https://openalex.org/W2099195351","https://openalex.org/W4256429076","https://openalex.org/W2012063272","https://openalex.org/W2348092930","https://openalex.org/W4312203868","https://openalex.org/W2138685729","https://openalex.org/W2062850566","https://openalex.org/W4308716484","https://openalex.org/W2090308851"],"abstract_inverted_index":{"The":[0],"estimation":[1,93,113],"of":[2,15,100,107,117],"phylogenetic":[3],"trees":[4,24,48,57,83],"for":[5,74],"individual":[6],"genes":[7],"or":[8],"multi-locus":[9,75],"datasets":[10],"is":[11],"a":[12,62],"basic":[13],"part":[14],"considerable":[16],"biological":[17],"research.":[18],"In":[19],"order":[20],"to":[21,25,72,89,103,114],"enable":[22],"large":[23,115,150],"be":[26],"computed,":[27],"Disjoint":[28],"Tree":[29],"Mergers":[30],"(DTMs)":[31],"have":[32,69],"been":[33,70],"developed;":[34],"these":[35,146],"methods":[36],"operate":[37],"by":[38],"dividing":[39],"the":[40,55,65,98,105,126],"input":[41,118],"sequence":[42],"dataset":[43],"into":[44,61],"disjoint":[45],"sets,":[46],"constructing":[47],"on":[49,64,149],"each":[50],"subset,":[51],"and":[52,133],"then":[53],"combining":[54],"subset":[56],"(using":[58],"auxiliary":[59],"information)":[60],"tree":[63,77,92,112],"full":[66],"dataset.":[67],"DTMs":[68,102],"used":[71],"advantage":[73],"species":[76,82,91],"estimation,":[78],"enabling":[79],"highly":[80],"accurate":[81],"at":[84],"reduced":[85],"computational":[86],"effort,":[87],"compared":[88],"leading":[90],"methods.":[94],"Here,":[95],"we":[96],"evaluate":[97],"feasibility":[99],"using":[101],"improve":[104],"scalability":[106],"maximum":[108],"likelihood":[109],"(ML)":[110],"gene":[111],"numbers":[116],"sequences.":[119],"Our":[120],"study":[121],"shows":[122,136],"distinct":[123],"differences":[124],"between":[125],"three":[127],"selected":[128],"ML":[129,147],"codes\u2014RAxML-NG,":[130],"IQ-TREE":[131],"2,":[132],"FastTree":[134],"2\u2014and":[135],"that":[137],"good":[138],"DTM":[139],"pipeline":[140],"design":[141],"can":[142],"provide":[143],"advantages":[144],"over":[145],"codes":[148],"datasets.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
