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Please refer following research article for more details:

• Kolekar P., Kale M., Kulkarni-Kale U., Alignment-free distance measure based on return time distribution for sequence analysis: Applications to 
  clustering, molecular phylogeny and subtyping, Molecular Phylogenetics and Evolution, (2012) 65(2): 510-522. [PMID: 22820020] 
  Download: Authors' preprint and Supplementary file

• Kolekar, Pandurang, Kale, Mohan, and Kulkarni-Kale, Urmila. Subtyping of Dengue Viruses using Return Time Distribution based Appproach. 
  Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2011.5590.1> (2011) 

• Kolekar P, Kale M, Kulkarni Kale U: Genotyping of Mumps viruses based on SH gene: Development of a server using alignment-free and 
  alignment-based methods. Immunome Research, 2011, 7(3):1-7 [PMID: 22126822]

Pictorial view of the RTD based alignment-free method for phylogenetic tree reconstruction at k=1