Distance based methods of DNA sequence analysis in phylogenetics

Alignment based methods are considered under NP hard problems they does not perform well when database becomes largeand complex. This paper discusses alignment free methods based on k-tuple, frequency and composition of bases and k-mer. All the methods are discussed taking pair of DNA sequence of same length and different length giving distance meaure between them. In the results we have shown all the discussed alignment free methods are almost same in calculating the distance measure of same length, but for different length sequences k-tuple based method and frequency and compositional based method's result are more close as compared to k-mer based method. Role of entropy in sequence analysis and various distance methods like Euclidean, Manhattan UPGMA and neighbor joining are also discussed.

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