From Gene Trees to Species Trees: Algorithms for Parsimonious Reconciliation

dc.contributor.advisorNakhleh, Luay K.
dc.creatorYu, Yun
dc.date.accessioned2013-03-08T00:40:19Z
dc.date.available2013-03-08T00:40:19Z
dc.date.issued2012
dc.description.abstractOne of the criteria for inferring a species tree from a collection of gene trees, when gene tree incongruence is assumed to be due to incomplete lineage sorting (ILS), is minimize deep coalescence , or MDC. Exact algorithms for inferring the species tree from rooted, binary trees under MDC were recently introduced. Nevertheless, in phylogenetic analyses of biological data sets, estimated gene trees may differ from true gene trees, be incompletely resolved, and not necessarily rooted. Further, the MDC criterion considers only the topologies of the gene trees. So the contributions of my work are three-fold: 1. We propose new MDC formulations for the cases in which the gene trees are unrooted/binary, rooted/non-binary, and unrooted/non-binary, prove structural theorems that allow me to extend the algorithms for the rooted/binary gene tree case to these cases in a straightforward manner. 2. We propose an algorithm for inferring a species tree from a collection of gene trees with coalescence times that takes into account not only the topology of the gene trees but also the coalescence times. 3. We devise MDC-based algorithms for cases in which multiple alleles per species may be sampled. We have implemented all of the algorithms in the PhyloNet software package and studied their performance in coalescent-based simulation studies in comparison with other methods including democratic vote, greedy consensus, STEM, and GLASS.
dc.format.extent82 p.en_US
dc.format.mimetypeapplication/pdf
dc.identifier.callnoTHESIS COMP.SCI. 2012 YU
dc.identifier.citationYu, Yun. "From Gene Trees to Species Trees: Algorithms for Parsimonious Reconciliation." (2012) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/70511">https://hdl.handle.net/1911/70511</a>.
dc.identifier.digitalYuYen_US
dc.identifier.urihttps://hdl.handle.net/1911/70511
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.subjectApplied sciences
dc.subjectBiological sciences
dc.subjectBioinformatics
dc.subjectComputer science
dc.titleFrom Gene Trees to Species Trees: Algorithms for Parsimonious Reconciliation
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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