Performing phylogenetic placement at scale

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.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Ecol, Evol, Conservation Biol

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Chu, Gillian

Contributors dc:contributor

• Warnow, Tandy

• phylogeny
• scalable
• phylogenetic placement

Statement dc:rights

• Copyright 2022 Gillian Chu

Language dc:language

en, eng

Handle dc:identifier

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

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F116252