Identifier

etd-05272015-141735

Degree

Master of Science in Computer Science (MSCS)

Department

Computer Science

Document Type

Thesis

Abstract

A phylogenetic tree is a tree like diagram showing the evolutionary relationship among various species based on their differences or similarity in their physical or genetic makeup.The similarity in their genetic makeup is traditionally measured based on pairwise distance between their gene sequences using sequence alignment methods. Due to the advancement in next generation sequencing technologies there is a huge amount of datasets available for partially or completely sequenced genomes. These massive datasets requires a faster comparison methods other than the traditional alignment-based approaches. Therefore, alignment free approaches are gaining popularity in recent years. In this thesis, we compare alignment-based and various alignment free methods for phylogenetic tree construction. The alignment free methods we study are based on k-mer frequency, Average Common Substring (ACS) and ACS with position restrictions and mismatches. The position restricted ACS is a novel contribution of this thesis. To evaluate performance of the alignment free approaches we applied it to phylogeny reconstruction using DNA ( 27 primate mitochondrial genomes) and protein (Starfish RNA-seq) sequence sets. The phylogenetic trees are constructed using Neighbor joining to the distance matrices obtained with the above mentioned alignment-free methods. The resulting phylogenetic trees are then compared with the reference tree using Branch Score Distance measure. Both the Neighbor joining and the Branch Score Distance Measure are calculated by using the programs neighbor and treedist from the PHYLIP package.

Date

2015

Document Availability at the Time of Submission

Secure the entire work for patent and/or proprietary purposes for a period of one year. Student has submitted appropriate documentation which states: During this period the copyright owner also agrees not to exercise her/his ownership rights, including public use in works, without prior authorization from LSU. At the end of the one year period, either we or LSU may request an automatic extension for one additional year. At the end of the one year secure period (or its extension, if such is requested), the work will be released for access worldwide.

Committee Chair

Shah, Rahul

DOI

10.31390/gradschool_theses.1087

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