University of Illinois Urbana-Champaign

Performing phylogenetic placement at scale

Chu, Gillian

Content Files
CHU-THESIS-2022.pdf

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https://hdl.handle.net/2142/116252

Description

Title
Performing phylogenetic placement at scale
Author(s)
Chu, Gillian
Issue Date
2022-07-19
Director of Research (if dissertation) or Advisor (if thesis)
Warnow, Tandy
Doctoral Committee Chair(s)
Warnow, Tandy
Department of Study
School of Integrative Biology
Discipline
Ecol, Evol, Conservation Biol
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
M.S.
Degree Level
Thesis
Keyword(s)
  • phylogeny
  • scalable
  • phylogenetic placement
Abstract
Phylogenetic placement is the problem of placing “query” sequences into an existing tree (called a “backbone tree”) whose leaves are aligned sequences, and has applications in updating large trees as well as in microbiome analysis. This is a study of phylogenetic placement pipelines which use extended alignment methods to first align the query sequence to the backbone alignment, before leveraging this information to place the query sequence into the tree using a placement method. We show that using methods specifically targeted for fragmentary sequences lead to higher accuracy, and we present pplacer-SCAMPP-taxtastic, which leverages several scalable techniques to extend the scalability of likelihood-based placement methods to ultra-large backbone trees (e.g., 200,000 sequences) with high accuracy.
Graduation Semester
2022-08
Type of Resource
Thesis
Handle URL
https://hdl.handle.net/2142/116252
Copyright and License Information
Copyright 2022 Gillian Chu

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