Analysis of genomes phylogeny using distance method based on similarity metric

An improved definition of the similarity metric based on the research of Professor Shihyen Chen is proposed, in order to solve the problem that the distances of mutual information and angle cosine do not satisfy the triangle inequality. The properties of proposed similarity metric are studied including the relationship with the distance. The phylogenetic trees of the genomes of 64 vertebrates are constructed by the method of composition vector and the distance based on similarity metric and mutual information or angle cosine. The results show that the distance of mutual information and angle cosine can be constructed by the improved definition of similarity metric, and the phylogenetic trees reconstructed by the constructed distance are agreement with the current known phylogenies of species.