Master of Science in Computer Science (MSCS)
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.
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Krishnan, Ambujam, "Phylogenetic Tree Construction for Starfish and Primate Genomes via Alignment Free Methods" (2015). LSU Master's Theses. 1087.