A New Distance-based Approach for Phylogenetic Analysis of Protein Sequences

With the availability of ever-increasing gene and protein sequence data across a large number of species, reconstruction of phylogenetic trees to reveal the evolutionary relationship among those species becomes more and more important. In this paper, we take the physicochemical properties of amino acids into account and introduce the protein feature sequences into phylogenetic analysis by using the Bhattacharyya distance. The phylogenetic trees on the two data sets have illustrated that the proposed approach performs equally well as the other methods do and is more efficient than some of the methods. So our method may be used to complement phylogenetic analysis.