A framework for alignment-free methods to perform similarity analysis of biological sequence

Comparing sequences is one of the important tasks in bioinformatics which helps in identifying evolutionary or structurally related protein or DNA sequence. The alignment problem has been studied for several decades for estimating phylogenies. But many recent studies have demonstrated considerable progress in improving the accuracy and reducing computational cost by alignment-free methods. In this paper we are proposing a unified framework to demonstrate, how the alignment-free methods are instrumental in elucidating the evolutionary relationships that exist among the species. Further, we have illustrated the steps involved in the proposed framework, on six beta-globin genes from six different species. The relationships are eventually represented by the phylogenetic tree. Similar phylogenetic trees are reconstructed after aligning sequences which offers high computational cost.