A simple feature representation vector for phylogenetic analysis of DNA sequences

In this study, a simple 4k-dimension feature representation vector is proposed to reconstruct phylogenetic trees, where k is the length of a word. The vector is composed of elements which characterize the relative difference of biological sequence from sequence generated by an independent random process. In addition, the variance of a vector which is obtained by averaging every column of feature representation matrix is employed to determine appropriate word length. In our experiments, reliable results can always be generated when word length is <7 which appears to be of lower computational complexity. Phylogenetic trees of 24 transferrins and 48 Hepatitis E viruses reconstructed at word length 6 are in good agreements with previous study, it shows that our method is efficient and powerful.