{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/110713"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/110713","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Disjoint Tree Mergers for large-scale maximum-likelihood tree estimation","abstract":"Embargo set by: Seth Robbins for item 118556 Lift date: 2023-09-17T02:34:57Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","abstract_html":"Embargo set by: Seth Robbins for item 118556 Lift date: 2023-09-17T02:34:57Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","abstract_has_math":false,"creators":["Park, Minhyuk"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Computer Science","degree_department":null,"school":null,"contributors":["Warnow, Tandy J"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2021,"date_issued":"2021-09-17T02:34:41Z","date_published":"2021-09-17T02:34:41Z","updated_at":"2026-07-22T22:24:52Z","subjects":["phylogeny estimation","maximum likelihood","RAxML","IQ-TREE","FastTree","cox1","heterotachy","disjoint tree mergers","Tree of Life"],"languages":["en"],"rights":["Copyright 2021 Minhyuk Park"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/110713","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Warnow, Tandy J"]},{"key":"dc:creator","label":"Author","values":["Park, Minhyuk"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2021-09-17T02:34:41Z","2023-09-17T02:34:57Z","2021-04-23","2021-05"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Computer Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["phylogeny estimation","maximum likelihood","RAxML","IQ-TREE","FastTree","cox1","heterotachy","disjoint tree mergers","Tree of Life"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2021 Minhyuk Park"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/110713"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Embargo set by: Seth Robbins for item 118556 Lift date: 2023-09-17T02:34:57Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only","Gene tree estimation is a biological problem that garners a lot of interest due to its ability to uncover evolutionary relationships in different genes which provides valuable insight into the hidden mechanisms of evolution. However, large-scale gene tree estimation has largely been unexplored, partially due to the limited available methods that can run on large datasets. Instead, a lot of effort has been focused on developing methods that are accurate on small to medium-sized datasets. We present a re-evaluation of divide-and-conquer pipelines on a variety of model conditions, including fragmentary sequences and heterogeneous evolution patterns, and show that our design of divide-and-conquer pipelines can consistently match or outperform FastTree and IQ-TREE with little overhead in runtime while matching or outperforming RAxML except on small datasets with very challenging model conditions. Furthermore, our divide-and-conquer pipeline is able to run on datasets that are too large for IQ-TREE or RAxML to handle.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-05-01","The student, Minhyuk Park, accepted the attached license on 2021-04-21 at 12:42.","The student, Minhyuk Park, submitted this Thesis for approval on 2021-04-21 at 12:43.","This Thesis was approved for publication on 2021-04-23 at 16:42.","DSpace SAF Submission Ingestion Package generated from Vireo submission #16464 on 2021-09-16 at 17:04:17","Made available in DSpace on 2021-09-17T02:34:41Z (GMT). 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However, large-scale gene tree estimation has largely been unexplored, partially due to the limited available methods that can run on large datasets. Instead, a lot of effort has been focused on developing methods that are accurate on small to medium-sized datasets. We present a re-evaluation of divide-and-conquer pipelines on a variety of model conditions, including fragmentary sequences and heterogeneous evolution patterns, and show that our design of divide-and-conquer pipelines can consistently match or outperform FastTree and IQ-TREE with little overhead in runtime while matching or outperforming RAxML except on small datasets with very challenging model conditions. Furthermore, our divide-and-conquer pipeline is able to run on datasets that are too large for IQ-TREE or RAxML to handle.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-05-01","The student, Minhyuk Park, accepted the attached license on 2021-04-21 at 12:42.","The student, Minhyuk Park, submitted this Thesis for approval on 2021-04-21 at 12:43.","This Thesis was approved for publication on 2021-04-23 at 16:42.","DSpace SAF Submission Ingestion Package generated from Vireo submission #16464 on 2021-09-16 at 17:04:17","Made available in DSpace on 2021-09-17T02:34:41Z (GMT). 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