Applications of heuristic search on phylogeny reconstruction problems

Warning The system is temporarily closed to updates for reporting purpose.

Mutluergil, Süha Orhun (2012) Applications of heuristic search on phylogeny reconstruction problems. [Thesis]

[thumbnail of SuhaOrhunMutluergil_440212.pdf] PDF
SuhaOrhunMutluergil_440212.pdf

Download (774kB)

Abstract

Phylogenies or evolutionary trees for a given family of species show the evolutionary relationships between these species. The leaves denote the given species, the internal nodes denote their common ancestors and the edges denote the genetic relationships. Species can be identified by their whole genomes and the evolutionary relations between species can be measured by the number of rearrangement events (i.e. mutations) that transform one genome into another. One approach to infer phylogeny from genomic data is by solving median genome problems for three genomes, or the genome rearrangement problem for pairs of genomes, while trying to minimize the total evolutionary distance among the given species. In this thesis, we have developed and implemented two search based algorithms for phylogeny reconstruction problem based on solving median genome problems for circular genomes of the same length without gene duplication. In order to show applicability and effectiveness of our algorithms, we have tested them with randomly generated instances and two real data sets: mitochondrial genomes of Metazoa and chloroplast genomes of Campanulaceae.
Item Type: Thesis
Uncontrolled Keywords: Phylogeny. -- Genome. -- Biological evolution. -- Phylogeny reconstruction. -- Median genome problem. -- Genome rearrangement. -- Inversion. -- Transposition. -- Filogeni. -- Ortanca genom problemi. -- Biyolojik evrim. -- Yeniden filojeni oluşturma. -- Genom yeniden dizilimi. -- Tersine çevirme. -- Yer değiştirme.
Subjects: T Technology > TK Electrical engineering. Electronics Nuclear engineering > TK7800-8360 Electronics > TK7885-7895 Computer engineering. Computer hardware
Divisions: Faculty of Engineering and Natural Sciences > Academic programs > Computer Science & Eng.
Faculty of Engineering and Natural Sciences
Depositing User: IC-Cataloging
Date Deposited: 02 Jul 2014 13:30
Last Modified: 26 Apr 2022 10:01
URI: https://research.sabanciuniv.edu/id/eprint/24290

Actions (login required)

View Item
View Item