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

• Main Author: Kalafi, Elham Yousef
• Format: Thesis
• Published: 2012
• Subjects: QH301 Biology
• Online Access: http://studentsrepo.um.edu.my/3843/1/abstract%2C_content.pdf; http://studentsrepo.um.edu.my/3843/2/Chap1_Intro%2C_Chap2_Lit_review.pdf; http://studentsrepo.um.edu.my/3843/3/Chap_3_Methods_and_Materials.pdf; http://studentsrepo.um.edu.my/3843/4/Chap4_Result%2C_Chap5Discussion%2C_Chap6_Conclusion.pdf; http://studentsrepo.um.edu.my/3843/5/References.pdf; http://pendeta.um.edu.my/client/default/search/results?qu=The+efficacy+of+alignment-based+and+alignment-free+methods+in+reconstructing+phylogenetic+trees+using+complete+mitochondrial+DNA+sequence&te=; http://studentsrepo.um.edu.my/3843/

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.