Distance measure is an important issue in phylogenetic analysis. Traditional measure approaches are time-consuming due to the fact that they require multiple sequence alignment, while the k-tuple distance is easy to compute and has been used in phylogenetic tree reconstruction. However, k-tuple distance is not effective for analysing identical sequences. Considering the occurrences of k-tuples and the sequence structure which may contain k-tuple locations as well as the order relation among them, we propose a new distance measure method to construct phylogenetic tree in this paper. The experimental results show that the new approach is capable of efficiently building phylogenetic trees.
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