The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi
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 alignme...
| _version_ | 1848772511474384896 |
|---|---|
| author | Kalafi, Elham Yousef |
| author_facet | Kalafi, Elham Yousef |
| author_sort | Kalafi, Elham Yousef |
| building | UM Research Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T13:27:41Z |
| format | Thesis |
| id | um-3843 |
| institution | University Malaya |
| institution_category | Local University |
| last_indexed | 2025-11-14T13:27:41Z |
| publishDate | 2012 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | um-38432013-08-22T08:30:30Z The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi Kalafi, Elham Yousef QH301 Biology 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. 2012 Thesis NonPeerReviewed application/pdf http://studentsrepo.um.edu.my/3843/1/abstract%2C_content.pdf application/pdf http://studentsrepo.um.edu.my/3843/2/Chap1_Intro%2C_Chap2_Lit_review.pdf application/pdf http://studentsrepo.um.edu.my/3843/3/Chap_3_Methods_and_Materials.pdf application/pdf http://studentsrepo.um.edu.my/3843/4/Chap4_Result%2C_Chap5Discussion%2C_Chap6_Conclusion.pdf application/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= 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. http://studentsrepo.um.edu.my/3843/ |
| spellingShingle | QH301 Biology Kalafi, Elham Yousef The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi |
| title | The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi |
| title_full | The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi |
| title_fullStr | The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi |
| title_full_unstemmed | The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi |
| title_short | The efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial DNA sequence / Elham Yousef Kalafi |
| title_sort | efficacy of alignment-based and alignment-free methods in reconstructing phylogenetic trees using complete mitochondrial dna sequence / elham yousef kalafi |
| topic | QH301 Biology |
| url | 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://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/3843/1/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 |