Investigations in phylogenetics: tree inference and model identifiability
dc.contributor.author | Yourdkhani, Samaneh | |
dc.date.accessioned | 2020-10-03T22:04:52Z | |
dc.date.available | 2020-10-03T22:04:52Z | |
dc.date.issued | 2020-05 | |
dc.identifier.uri | http://hdl.handle.net/11122/11303 | |
dc.description | Dissertation (Ph.D.) University of Alaska Fairbanks, 2020 | en_US |
dc.description.abstract | This thesis presents two projects in mathematical phylogenetics. The first presents a new, statistically consistent, fast method for inferring species trees from topological gene trees under the multispecies coalescent model. The algorithm of this method takes a collection of unrooted topological gene trees, computes a novel intertaxon distance from them, and outputs a metric species tree. The second establishes that numerical and non-numerical parameters of a specic Prole Mixture Model of protein sequence evolution are generically identifiable. Algebraic techniques are used, especially a theorem of Kruskal on tensor decomposition. | en_US |
dc.description.tableofcontents | Chapter 1: Introduction. Chapter 2: Inferring Species Tree from Gene Trees -- 2.1 Introduction -- 2.2 Background and Notation -- 2.3 Weighted Rooted Triple Metrization of a Rooted Tree -- 2.4 Weighted Quartet Metrization of an Unrooted Tree -- 2.5 Weighted Quartet Distance Supertree and Consensus Algorithms -- 2.6 Algorithm Performance in Simulations -- References. Chapter 3: Identiability of a Protein Model -- 3.1 Abstract -- 3.2 Introduction -- 3.3 Markov Models on Trees -- 3.4 Algebraic Denitions and Lemmas -- 3.4.1 Denitions -- 3.4.2 Rank Propositions -- 3.5 Algebraic Aspects of the Prole Mixture Model -- 3.6 Identiability of Parameters for the Prole Mixture Model -- 3.7 Some other results -- References. Chapter 4: Conclusion and Future Work -- References -- Appendix. | en_US |
dc.language.iso | en_US | en_US |
dc.subject | phylogeny | en_US |
dc.subject | mathematical models | en_US |
dc.subject | evolutionary genetics | en_US |
dc.subject | biology | en_US |
dc.subject | computational biology | en_US |
dc.title | Investigations in phylogenetics: tree inference and model identifiability | en_US |
dc.type | Dissertation | en_US |
dc.type.degree | phd | en_US |
dc.identifier.department | Department of Mathematics and Statistics | en_US |
dc.contributor.chair | Rhodes, John A. | |
dc.contributor.chair | Allman, Elizabeth S. | |
dc.contributor.committee | McIntyre, Julie | |
dc.contributor.committee | Williams, Gordon | |
refterms.dateFOA | 2020-10-03T22:04:52Z |