Tabu Search and Genetic Algorithm for Phylogeny Inference

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dc.contributor.advisor Shu-Cherng Fang, Committee Chair en_US
dc.contributor.advisor Jeffrey L. Thorne, Committee Co-Chair en_US
dc.contributor.advisor Henry L. W. Nuttle, Committee Member en_US
dc.contributor.advisor Steffen Heber, Committee Member en_US Lin, Yu-Min en_US 2010-04-02T18:25:31Z 2010-04-02T18:25:31Z 2008-10-21 en_US
dc.identifier.other etd-10092008-235130 en_US
dc.description.abstract Phylogenetics is the study of evolutionary relations between different organisms. Phylogenetic trees are the representations of these relations. Researchers have been working on finding fast and systematic approaches to reconstruct phylogenetic trees from observed data for over 40 years. It has been shown that, given a certain criterion to evaluate each tree, finding the best fitted phylogenetic trees among all possible trees is an NP-hard problem. In this study, we focus on the topology searching techniques for the maximum-parsimony and maximum-likelihood phylogeny inference. We proposed two search methods based on tabu search and genetic algorithms. We first explore the feasibility of using tabu search for finding the maximum-parsimony trees. The performance of the proposed algorithm is evaluated based on its efficiency and accuracy. Then we proposed a hybrid method of the tabu search and genetic algorithm. The experimental results indicate that the hybrid method can provide maximum-parsimony trees with a ggood level of accuracy and efficiency. The hybrid method is also implemented for finding maximum-likelihood trees. The experimental results show that the proposed hybrid method produce better maximum-likelihood trees than the default-setting dnaml program in average on the tested data sets. On a much larger data set, the hybrid method outperforms the default-setting dnaml program and has equally good performance as the dnaml program with the selected jumble option. en_US
dc.rights I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dis sertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to NC State University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. en_US
dc.subject parsimony en_US
dc.subject phylogeny en_US
dc.subject genetic algorithm en_US
dc.subject tabu search en_US
dc.subject topology search en_US
dc.subject maximum likelihood en_US
dc.title Tabu Search and Genetic Algorithm for Phylogeny Inference en_US PhD en_US dissertation en_US Operations Research en_US

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