Abstract
We suggest a new 2D graphical representation of DNA sequences using adjacent nucleotide pairs. The representation is more informative and sensitive as it is based on the chemical properties of nucleotides. We have implemented and tested our method on two different real sequence sets. The results obtained are consistent with those in the literature. We also present a new way to compare alignment-free methods on simulated sequences with known true history. The proposed method is compared with two other recently proposed alignment-free methods. Satisfactory results have been found for sets having large number of sequences.
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