Performing phylogenetic placement at scale

Chu, Gillian

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

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

Copyright and License Information

Copyright 2022 Gillian Chu

Owning Collections