A number of methods without sequence alignment for deriving species phylogeny based on overall similarities of complete genomes have been developed. These include fractal analysis [2] [3] [4] , dynamical language model [5] , information-based analysis [6] [7] [8] , log-correlation distance and Fourier transformation with Kullback-Leibler divergence distance [9] , Markov model [10] [11] [12] [13] [14] [15] , principal component analysis [16] and singular value decomposition (SVD) [17] [18] [19] . The analyses based on the Markov model and dynamical language model without sequence alignment using 103 prokaryotes and 6 eukaryotes have yielded trees separating the three domains of life, Archaea, Eubacteria and Eukarya, with the relationships among the taxa consistent with those based on traditional analyses [5, 11] . These two methods were also used to analyze the complete chloroplast genomes [5, 12] . The SVD method was used to analyze mitochondrial genomes of 64 selected vertebrates [19] . A correlation-distance method without removing the random background (similar to [7] ) was used to analyze rRNA gene sequences as DNA barcodes [20] .