<mods:mods xmlns:mods="http://www.loc.gov/mods/v3" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-4.xsd"><mods:titleInfo><mods:title>Improving Information Propagation in Phylogenetic Workflows</mods:title></mods:titleInfo><mods:name type="personal"><mods:namePart>Guang, August</mods:namePart><mods:role><mods:roleTerm type="text">creator</mods:roleTerm></mods:role></mods:name><mods:name type="personal"><mods:namePart>Lawrence, Charles</mods:namePart><mods:role><mods:roleTerm type="text">Advisor</mods:roleTerm></mods:role></mods:name><mods:name type="personal"><mods:namePart>Dunn, Casey</mods:namePart><mods:role><mods:roleTerm type="text">Reader</mods:roleTerm></mods:role></mods:name><mods:name type="personal"><mods:namePart>Lewis, Paul</mods:namePart><mods:role><mods:roleTerm type="text">Reader</mods:roleTerm></mods:role></mods:name><mods:name type="corporate"><mods:namePart>Brown University. Department of Applied Mathematics</mods:namePart><mods:role><mods:roleTerm type="text">sponsor</mods:roleTerm></mods:role></mods:name><mods:originInfo><mods:copyrightDate>2018</mods:copyrightDate></mods:originInfo><mods:physicalDescription><mods:extent>xiv, 100 p.</mods:extent><mods:digitalOrigin>born digital</mods:digitalOrigin></mods:physicalDescription><mods:note type="thesis">Thesis (Ph. D.)--Brown University, 2018</mods:note><mods:genre authority="aat">theses</mods:genre><mods:abstract>Despite the enormous amount of biological variation and technical uncertainty&#13;
in sequence data, most phylogenetic workflows propagate a single point estimate&#13;
throughout the numerous analysis components, and only in a forward direction. This&#13;
approach relies on three implicit assumptions: (i) the order of the analysis steps is biologically&#13;
justified, (ii) a Markovian dependency structure exists between analysis&#13;
components, and (iii) there is low relative entropy between results at each analysis&#13;
step. There is evidence that these assumptions, in particular low relative entropy, are&#13;
frequently violated in empirical studies with potential detrimental effects in phylogenetic&#13;
analyses.&#13;
&#13;
In this thesis, I lay out a probabilistic framework that provides a unified perspective&#13;
to provide context for evaluating priorities for future developments of methods and&#13;
tools. I then develop a generative model of the natural and technical processes that&#13;
produce observed genomic reads within the framework that can be used to assess and&#13;
validate approaches that relax the implicit assumptions. Finally, I explore two ways to&#13;
accommodate and propagate more information in a phylogenetic workflow. The first&#13;
way, an HMM profile-sampling approach to genome assembly, relaxes the assumption&#13;
of low relative entropy in results from the genome assembly analysis component.&#13;
This approach finds relevant applications to HIV transmission networks. The second&#13;
way, an iterative approach to identifying and resolving transcriptome assembly errors,&#13;
capitalizes on the assumption of Markovian dependence.</mods:abstract><mods:subject><mods:topic>HIV/AIDS</mods:topic></mods:subject><mods:subject><mods:topic>Probability</mods:topic></mods:subject><mods:subject authority="fast" authorityURI="http://id.worldcat.org/fast" valueURI="http://id.worldcat.org/fast/00871990"><mods:topic>Computational biology</mods:topic></mods:subject><mods:subject authority="fast" authorityURI="http://id.worldcat.org/fast" valueURI="http://id.worldcat.org/fast/01062326"><mods:topic>Phylogeny</mods:topic></mods:subject><mods:language><mods:languageTerm authority="iso639-2b">English</mods:languageTerm></mods:language><mods:recordInfo><mods:recordContentSource authority="marcorg">RPB</mods:recordContentSource><mods:recordCreationDate encoding="iso8601">20180615</mods:recordCreationDate></mods:recordInfo><mods:identifier type="doi">10.26300/m4j5-dd88</mods:identifier><mods:accessCondition type="rights statement" xlink:href="http://rightsstatements.org/vocab/InC/1.0/">In Copyright</mods:accessCondition><mods:accessCondition type="restriction on access">Collection is open for research.</mods:accessCondition><mods:typeOfResource authority="primo">dissertations</mods:typeOfResource></mods:mods>