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Evolutionary Tree, Hierarchical Clustering, Bioinformatics, Codons, mtDNA

Large-scale analysis of genome sequences is in progress around the world, the major application of which is to establish the evolutionary relationship among the species using phylogenetic trees. Hierarchical agglomerative algorithms can be used to generate such phylogenetic trees given the distance matrix representing the dissimilarity among the species. ClustalW and Muscle are two general purpose programs that generates distance matrix from the input DNA or protein sequences. The limitation of these programs is that they are based on Smith-Waterman algorithm which uses dynamic programming for doing the pair-wise alignment. This is an extremely time consuming process and the existing systems may even fail to work for larger input data set. To overcome this limitation, we have used the frequency of codons usage as an approximation to find dissimilarity among species. The proposed technique further reduces the complexity by extracting only the significant features of the species from the mtDNA sequences using the techniques like frequent codons, codons with maximum range value or PCA technique. We have observed that the proposed system produces nearly accurate results in a significantly reduced running time.