Comparison of alignment-free methods based on mitochondrion complete genome

In molecular biology, the Alignment-based methods are widely applied to phylogemc analysis. However, there are some limits for this kind of methods. In this paper we introduce a new kind of Alignment-free methods, which is with less influences of subjective factors and gene reshuffle, and the most important, its computational complexity is O(L) where L is the length of sequences. The FDOD method, which is one of the Alignment-free methods, has been proposed for phylogemc analysis by us recently. We use the new method in the study of phylogenic analysis of mitochondrion complete genome and Cytb of mammalian to compare it with other methods including both Alignment - base and Alignment-free. The result of the new method FDOD is more consistent with the one in traditional taxonomy than those of other methods. In addition, we also find that FDOD do better than traditional Kimura-2-parameters Distance to unite members of the same order into one or few branches.