{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/115569"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/115569","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"SCAMPP: Scalable alignment-based phylogenetic placement","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01","abstract_has_math":false,"creators":["Wedell, Eleanor"],"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"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-05","date_published":"2022-05","updated_at":"2026-07-22T22:24:54Z","subjects":["Phylogenetic placement","Maximum likelihood","Phylogenetics","pplacer","EPA-ng"],"languages":["en","eng"],"rights":["Copyright 2022 Eleanor Wedell"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/115569","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Warnow, Tandy"]},{"key":"dc:creator","label":"Author","values":["Wedell, Eleanor"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-05","2022-04-25"]},{"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":["Phylogenetic placement","Maximum likelihood","Phylogenetics","pplacer","EPA-ng"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2022 Eleanor Wedell"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/115569"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01","The student, Eleanor Wedell, accepted the attached license on 2022-04-18 at 14:02.","The student, Eleanor Wedell, submitted this Thesis for approval on 2022-04-18 at 14:17.","This Thesis was approved for publication on 2022-04-25 at 16:12.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17756 on 2022-11-11 at 12:06:04","Phylogenetic placement, the problem of placing a \"query” sequence into a precomputed phylogenetic “backbone” tree, is useful for constructing large trees, performing taxon identification of newly obtained sequences, and other applications. The most accurate current methods, such as pplacer and EPA-ng, are based on maximum likelihood and require that the query sequence be provided within a multiple sequence alignment that includes the leaf sequences in the backbone tree. This approach enables high accuracy but also makes these likelihood-based methods computationally intensive on large backbone trees, and can even lead to them failing when the backbone trees are very large (e.g., having 50,000 or more leaves). We present SCAMPP (SCAlable alignMent-based Phylogenetic Placement), a technique to extend the scalability of these likelihood-based placement methods to ultra-large backbone trees. We show that pplacer-SCAMPP and EPA-ng-SCAMPP both scale well to ultra-large backbone trees (even up to 200,000 leaves), with accuracy that improves on APPLES and APPLES-2, two recently developed fast phylogenetic placement methods that scale to ultra-large datasets. EPA-ng-SCAMPP and pplacer-SCAMPP are available at https://github.com/chry04/PLUSplacer."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["SCAMPP: Scalable alignment-based phylogenetic placement"]}]}],"canonical_facts":{"dc:contributor":["Warnow, Tandy"],"dc:creator":["Wedell, Eleanor"],"dc:date":["2022-05","2022-04-25"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01","The student, Eleanor Wedell, accepted the attached license on 2022-04-18 at 14:02.","The student, Eleanor Wedell, submitted this Thesis for approval on 2022-04-18 at 14:17.","This Thesis was approved for publication on 2022-04-25 at 16:12.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17756 on 2022-11-11 at 12:06:04","Phylogenetic placement, the problem of placing a \"query” sequence into a precomputed phylogenetic “backbone” tree, is useful for constructing large trees, performing taxon identification of newly obtained sequences, and other applications. The most accurate current methods, such as pplacer and EPA-ng, are based on maximum likelihood and require that the query sequence be provided within a multiple sequence alignment that includes the leaf sequences in the backbone tree. This approach enables high accuracy but also makes these likelihood-based methods computationally intensive on large backbone trees, and can even lead to them failing when the backbone trees are very large (e.g., having 50,000 or more leaves). We present SCAMPP (SCAlable alignMent-based Phylogenetic Placement), a technique to extend the scalability of these likelihood-based placement methods to ultra-large backbone trees. We show that pplacer-SCAMPP and EPA-ng-SCAMPP both scale well to ultra-large backbone trees (even up to 200,000 leaves), with accuracy that improves on APPLES and APPLES-2, two recently developed fast phylogenetic placement methods that scale to ultra-large datasets. EPA-ng-SCAMPP and pplacer-SCAMPP are available at https://github.com/chry04/PLUSplacer."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/115569"],"dc:language":["en","eng"],"dc:rights":["Copyright 2022 Eleanor Wedell"],"dc:subject":["Phylogenetic placement","Maximum likelihood","Phylogenetics","pplacer","EPA-ng"],"dc:title":["SCAMPP: Scalable alignment-based phylogenetic placement"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Computer Science"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:54Z"}