Construction of Phylogenetic Trees
We are thankful to Almighty Allah for his blessings for the successful completion of our thesis. Our heartiest gratitude, profound indebtedness and deep respect go to our supervisor, Professor Dr. Md. Saidur Rahman, Department of Computer Science and Engineering, Military Institute of Science and...
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| Główni autorzy: | , |
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| Format: | Praca dyplomowa |
| Język: | angielski |
| Wydane: |
2015
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| Hasła przedmiotowe: | |
| Dostęp online: | http://hdl.handle.net/123456789/103 |
| Etykiety: |
Nie ma etykietki, Dołącz pierwszą etykiete!
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| _version_ | 1868226960945053696 |
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| author | Tahira, Afifa Rifat, Md. Farhan Tanveer |
| author_browse | Rifat, Md. Farhan Tanveer Tahira, Afifa |
| author_facet | Tahira, Afifa Rifat, Md. Farhan Tanveer |
| author_sort | Tahira, Afifa |
| collection | DSpace |
| description | We are thankful to Almighty Allah for his blessings for the successful completion of our
thesis. Our heartiest gratitude, profound indebtedness and deep respect go to our supervisor,
Professor Dr. Md. Saidur Rahman, Department of Computer Science and Engineering,
Military Institute of Science and Technology (MIST), Dhaka-1216, for his constant supervision,
affectionate guidance and great encouragement and motivation. His keen interest on
the topic and valuable advices throughout the study was of great help in completing thesis.
We are especially grateful to the Department of Computer Science and Engineering (CSE)
of Military Institute of Science and Technology (MIST) for providing their all out support
during the thesis work.
Finally, we would like to thank our families and our course mates for their appreciable
assistance, patience and suggestions during the course of our thesis
. |
| format | Thesis |
| id | oai:localhost:123456789-103 |
| institution | My University |
| language | English |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| record_format | dspace |
| spelling | oai:localhost:123456789-1032015-06-28T04:58:17Z Construction of Phylogenetic Trees Tahira, Afifa Rifat, Md. Farhan Tanveer : Phylogenetic, Triplet, Algorithm AllRTC, Terminology . We are thankful to Almighty Allah for his blessings for the successful completion of our thesis. Our heartiest gratitude, profound indebtedness and deep respect go to our supervisor, Professor Dr. Md. Saidur Rahman, Department of Computer Science and Engineering, Military Institute of Science and Technology (MIST), Dhaka-1216, for his constant supervision, affectionate guidance and great encouragement and motivation. His keen interest on the topic and valuable advices throughout the study was of great help in completing thesis. We are especially grateful to the Department of Computer Science and Engineering (CSE) of Military Institute of Science and Technology (MIST) for providing their all out support during the thesis work. Finally, we would like to thank our families and our course mates for their appreciable assistance, patience and suggestions during the course of our thesis . A phylogenetic tree is an unordered, distinctly leaf-labeled tree which shows evolutionary relationship among the leaves that represent the species. Inferring phylogenies using computational methods has several important applications in biological and biochemical research. Drug discovery and conservation biology are such examples. Phylogenetic trees have some important applications in practical fields, such as forensics, gene and protein function detection and drug design. In Bioinformatics, computation of the Tree of Life considering all living beings on earth is a grand challenge, in which phylogenetic tree can play important role to derive such relations. Phylogenetic tree construction from valid triplet set is one of the most common approaches of construction till date. A valid triplet set consists of a number of rooted triplets which are individually a phylogenetic tree of three leaves. Aho et al: first investigate the problem and later other researchers gradually meliorate and enrich his idea. These great research works solve many problems as well as introduce some open problems related to phylogenetic tree construction. Such a problem is to construct a phylogenetic tree consistent with all triplets in the given triplet set. Experimentally obtained data may contain incorrect information which results in erroneous triplet set, and thus maximum rooted triplet consistency (MaxRTC) is maintained in this case. During phylogenetic tree construction, maintenance of MaxRTC, sometimes ignores some important triplets where loss of information occurs. Moreover, the tree constructed from the triplet set contains unevenly distributed species. In this thesis, we study different aspects of the problem and introduce a heuristic algorithm to construct phylogenetic tree on all the triplets in the triplet set by making a small number of corrections on the triplets, where approximately even distribution of species is ensured. For a given set of m triplets with n species, this algorithm runs in O(m n) time. Though the algorithm is less efficient, the loss of information is less here than previous algorithms. On the other hand, checking the consistency of the triplet in a phylogenetic tree is another important problem in the field of phylogenetics. It is useful to compare two phylogenetic trees and measure the dissimilarity between them to check the accuracy. So it is very important to check this consistency in minimum amount of time. In this thesis, we give an algorithm to check the consistency of the triplet in constant time. This algorithm requires an initialization stage of time complexity O(n2) that preprocess the phylogenetic tree. Then we check if the triplet satisfies the phylogenetic tree or not in O(1) time. Though the initial complexity is high, the algorithm is helpful because it can check the consistency of a triplet in constant time. 2015-06-28T03:32:14Z 2015-06-28T03:32:14Z 2015-06-28 Thesis http://hdl.handle.net/123456789/103 en application/pdf |
| spellingShingle | : Phylogenetic, Triplet, Algorithm AllRTC, Terminology . Tahira, Afifa Rifat, Md. Farhan Tanveer Construction of Phylogenetic Trees |
| title | Construction of Phylogenetic Trees |
| title_full | Construction of Phylogenetic Trees |
| title_fullStr | Construction of Phylogenetic Trees |
| title_full_unstemmed | Construction of Phylogenetic Trees |
| title_short | Construction of Phylogenetic Trees |
| title_sort | construction of phylogenetic trees |
| topic | : Phylogenetic, Triplet, Algorithm AllRTC, Terminology . |
| url | http://hdl.handle.net/123456789/103 |
| work_keys_str_mv | AT tahiraafifa constructionofphylogenetictrees AT rifatmdfarhantanveer constructionofphylogenetictrees |