Alignment-free sequence comparison using joint frequency and position information of k-words

This paper proposes a novel alignment-free sequence comparison method to identify the genetic relationships of organisms with a high resolution. For an accurate comparison, both frequency and position information of k-words are obtained from genome sequences in the proposed alignment-free sequence comparison method. Using principal component analysis (PCA) and phylogeny analysis, we identify the classification performance of proposed method. Then, the phylogenetic trees of proposed and conventional schemes are compared with reliable reference tree.