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Title: Efficient Algorithms for the Gene Tree-Species Tree Reconciliation Problem
Authors: ZHENG YU
Keywords: algorithms gene-tree species-tree reconciliation non-binary refinement
Issue Date: 15-Aug-2014
Citation: ZHENG YU (2014-08-15). Efficient Algorithms for the Gene Tree-Species Tree Reconciliation Problem. ScholarBank@NUS Repository.
Abstract: Gene tree and species tree reconciliation is an important method in comparative genomics. A gene tree which represents the evolutionary history of a gene family is often discordant with the corresponding species tree due to complicated gene evolution history. Thus, a gene tree is reconciled with the corresponding species tree to infer gene evolutionary events, to annotate the relationships between genes, and to reconstruct the evolutionary history of species. In this thesis, motivated by the fact that reference species trees and real gene trees are often non-binary, we investigate various issues of reconciliation for non-binary trees. We first design efficient algorithms for the gene tree refinement problem in different reconciliation models. We then study the species tree refinement problem for non-binary gene tree under the duplication cost model. Simulation study shows that our algorithms are fast and hence more suitable for genome-scale study.
Appears in Collections:Ph.D Theses (Open)

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