The whole DNA sequences (including protein-coding and non-coding regions), all protein-coding DNA sequences and the amino acid sequences of all protein-coding genes from genome data are used for phylogenetic analysis. For Dataset 1, we have seen that amino acid sequences of all protein-coding genes from genomes give better results than those given by the whole DNA sequences and all proteincoding DNA sequences. We evaluated the dynamical language approach with chord distance and piecewise distance on the amino acid sequences of all protein-coding genes from genomes for K = 3, 4, 5 and 6. We find the trees using the new distance metrics have the same topology as the trees using the old "distance" for the same value of K, and the trees for K = 6 are the best. Here we present the tree for K = 6 using dynamical language approach with chord distance in Figure 2 . The phylogeny shown in Figure 2 supports the broad division into three domains and agrees with the tree of life based on 16S rRNA in a majority of basic branches. For further biological discussions, one can refer to [5] with the correction for the position of Pyrobaculum aerophilum (Pyrae). For Dataset 2, we have seen that the amino acid sequences of all protein-coding genes from genomes give better results than those given by the whole DNA sequences and all protein-coding DNA sequences. We evaluated the dynamical language approach with chord distance and piecewise distance on the amino acid sequences of all protein-coding genes from genomes for K = 3, 4, 5 and 6. We find the tree using the piecewise distance has the same topology as the tree using the old "distance" for the same value of K, the tree using the chord distance has similar topology (a little bit worse because Pinus thunbergii is separated from its correct position) to the tree using the old "distance" for the same value of K. And the trees of K = 6 are the best. Hence we present the tree for K = 6 using the dynamical language approach with piecewise distance ( 3 = ρ ) in Figure 3 . We also note that the topology of the tree in Figure 3 is the same as that of the tree obtained by the Markov model in [12] ). The phylogeny of Figure 3 shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution. For further biological discussions, one can refer to [12] . Genomes" on http://www.genome.jp/kegg/genes.html)), we find that the whole DNA sequences give better results than those given by the amino acid sequences of all protein-coding genes from genomes and all protein-coding DNA sequences. We evaluated the dynamical language approach with the proposed distance metrics on the sequences of whole genomes for K = 6 to 13. We find the tree using the piecewise distance has the same topology as the tree using the old "distance" for the same value of K, the tree using the chord distance has similar topology (a little bit better because Dasypus novemcinctus.(Dnov) is close to but does not remain in a branch of primates) to the tree using the old "distance" for the same value of K. And the trees for K = 11 are the best. Hence we present the tree for K = 11 using the dynamical language approach with chord distance in Figure 4 . The tree ( Figure 4 ) generated is similar in topology to the tree obtained using the SVD method in the case 4 = K [19] , and is also similar to a recently generated tree of 69 species [33] , placing a vast majority of species into well-accepted groupings. As shown in Figure 4 , our distance-based analysis shows that the mitochondrial genomes are separated into three major clusters. One group corresponds to mammals; one group corresponds to the fish; and the third one represents Archosauria (including birds and reptiles). The interrelationships among the mitochondrial genomes are roughly in agreement with the current understanding of the phylogeny of vertebrates revealed by the traditional approaches. For further biological discussion, one can refer to [32] .