The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi

Kalafi, Elham Yousef (2012) The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi. Masters thesis, University of Malaya.

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            Abstract

            Similarity searching tools are generally divided to two distinct groups: Alignment-based and alignment-free methods. There is no standard comparison between alignment-based and alignment-free methods` performance. In this project, I compared CLUSTALW, T-COFFEE and MUSCLE algorithms with four alignment-free methods, Kr, D2, D2z and MplusD to find out which of these methods are more efficient with respect to time and accuracy. In both alignment-based and alignment-free, results are represented by phylogenetic trees. Here, all phylogenetic trees are compared against the reference tree to determine how accurate the methods are. I found that alignment-based methods were the most accurate comparing to alignment-free methods. On the other hand, Kr and D2z gave approximately correct results with substantial gain in speed. I conclude that for inferring phylogenetic trees containing taxa that have diverged for a long time, alignment-based methods should be used. However if many closely related species are studied, then an alignment-free method should worth well.

            Item Type: Thesis (Masters)
            Additional Information: Dissertation submitted in fulfilment of the requirement for the degree of Master of Science
            Uncontrolled Keywords: Alignment-based methods; Alignment-free methods; Mitochondrial DNA sequence
            Subjects: Q Science > QH Natural history > QH301 Biology
            Divisions: Faculty of Science
            Depositing User: Ms Rabiahtul Adauwiyah
            Date Deposited: 27 Mar 2013 15:29
            Last Modified: 22 Aug 2013 16:30
            URI: http://studentsrepo.um.edu.my/id/eprint/3843

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