Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer

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dc.contributor.advisorNakhleh, Luay K.
dc.creatorRuths, Derek A.
dc.date.accessioned2009-06-04T08:04:28Z
dc.date.available2009-06-04T08:04:28Z
dc.date.issued2006
dc.description.abstractIn bacteria and viruses, recombination and horizontal gene transfer (HGT) permit the direct exchange or acquisition of DNA into the genome from species other than the "parent". Two major challenges face attempts at reconstructing non-treelike evolution: (1) multiple sources of gene tree incongruence exist, making various reconciliation scenarios possible, and (2) reconstructing a given reconciliation scenario is computationally hard. In this thesis, we address the latter problem, describing new methods for reconstructing recombination and HGT events: RECOMP and RIATA-HGT. RECOMP is a recombination detection method, faster than all existing algorithms and as accurate as the best. RIATA-HGT is the first polynomial-time heuristic that reconstructs unrestricted HGT events based on gene tree incongruence. We also describe two studies characterizing the sources of statistical error in phylogenetic incongruence: ortholog inference and phylogeny estimation. These studies identify computational problems whose revision will improve the overall accuracy of phylogenetic incongruence-based, non-treelike evolution reconstruction tools.
dc.format.extent90 p.en_US
dc.format.mimetypeapplication/pdf
dc.identifier.callnoTHESIS COMP.SCI. 2006 RUTHS
dc.identifier.citationRuths, Derek A.. "Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer." (2006) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/17912">https://hdl.handle.net/1911/17912</a>.
dc.identifier.urihttps://hdl.handle.net/1911/17912
dc.language.isoeng
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.
dc.subjectGenetics
dc.subjectComputer science
dc.subjectBiology
dc.titleApplications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer
dc.typeThesis
dc.type.materialText
thesis.degree.departmentComputer Science
thesis.degree.disciplineEngineering
thesis.degree.grantorRice University
thesis.degree.levelMasters
thesis.degree.nameMaster of Science
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