2026-09-21T15:41:49Z https://www.ideals.illinois.edu/oai-pmh

oai:www.ideals.illinois.edu:2142/110713 2023-07-11 col_2142_5131 col_2142_10761 com_2142_5130 com_2142_10755 com_2142_234

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 application/pdf http://hdl.handle.net/2142/110713 en Copyright 2021 Minhyuk Park phylogeny estimation maximum likelihood RAxML IQ-TREE FastTree cox1 heterotachy Warnow, Tandy J Park, Minhyuk 2021-09-17T02:34:41Z 2021-09-17T02:34:41Z 2023-09-17T02:34:57Z 2021-04-23 2021-05 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). No. of bitstreams: 2 PARK-THESIS-2021.pdf: 370186 bytes, checksum: 33203f5ea5bfbb0ce0f610d63924768f (MD5) LICENSE.txt: 4209 bytes, checksum: 2128a1547ead52147cb6ec6de1f791fc (MD5) Previous issue date: 2021-04-23 disjoint tree mergers Tree of Life Disjoint Tree Mergers for large-scale maximum-likelihood tree estimation text Thesis Computer Science Computer Science University of Illinois at Urbana-Champaign Thesis M.S.