k-mers. The time refers to the number of residues in successive appearance of particular k-mer. Thus the occurrence of each k-mer in a sequence is calculated in the form of RTD, which is then summarised using two statistical parameters mean (μ) and standard deviation (σ). Thus each sequence is represented in the form of numeric vector of size 2⋅4k containing μ and σ of 4k RTDs. The pair wise distance between sequences is calculated using Euclidean distance measure. The distance matrix thus obtained can be used to construct phylogenetic tree using clustering algorithms like neighbor-joining, UPGMA etc. A recent approach Pattern Extraction through Entropy Retrieval (PEER) provides direct detection of the k-mer length and summarised the occurrence interval using entropy.
