A novel k-word relative measure for sequence comparison

• The new normalized k-word average relative distance is proposed in this paper.
• A new method is suggested to reduce the matrix dimension, can greatly lessen the amount of calculation and operation time.
• The phylogenetic trees is plotted based on the new normalized k-word average relative distance.
• The AUC is calculated to test the effectiveness of this new distance.

In order to extract phylogenetic information from DNA sequences, the new normalized k-word average relative distance is proposed in this paper. The proposed measure was tested by discriminate analysis and phylogenetic analysis. The phylogenetic trees based on the Manhattan distance measure are reconstructed with k ranging from 1 to 12. At the same time, a new method is suggested to reduce the matrix dimension, can greatly lessen the amount of calculation and operation time. The experimental assessment demonstrated that our measure was efficient. What's more, comparing with other methods’ results shows that our method is feasible and powerful for phylogenetic analysis.

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