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.
| Identifer | oai:union.ndltd.org:NCSU/oai:NCSU:etd-10092008-235130 |
| Date | 21 October 2008 |
| Creators | Lin, Yu-Min |
| Contributors | Shu-Cherng Fang, Jeffrey L. Thorne, Henry L. W. Nuttle, Steffen Heber |
| Publisher | NCSU |
| Source Sets | North Carolina State University |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://www.lib.ncsu.edu/theses/available/etd-10092008-235130/ |
| Rights | unrestricted, 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. |
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