A method for constructing phylogenetic tree based on k-mer information

With the success in the sequencing of complete genomes, the phylogenetics analysis by alignment-free methods based on complete genomes has been a hot topic. The nucleotide composition is different across species or populations. The information in the genetic language-DNA can be reflected largely in its k-mer frequencies. The phylogenetic tree based on k-mer frequencies would provide us the evolutionary relation among organisms from a novel perspective. In this study, the genomes of 84 large viruses are characterized by an information parameter, which is defined based on k-mer frequencies in the sequences; then the distances among the virus genomes are calculated and a phylogenetic tree is constructed for the viruses by using neighbor-joining method. The obtained phylogenetic tree is largely in agreement with the others’ tree.