Sequence comparison using multi-order Markov chains

DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are then used to compute pair-wise distances; and the consequent distances are used to construct molecular phytogeny. Experiments with both simulated and real dataseis show that the proposed method is able to reconstruct phylogenies consistent with those pre-defined or commonly accepted phylogenies.