jD2Stat: an alignment-free tool for generating pairwise distances of molecular sequences

jD2Stat (previously known as JIWA*) is a Java package that utilises a series of D₂ statistics to extract k-mers (subsequences at defined k length) from a set of biological sequences, and generate pairwise distances for each possible pair. This distance can be used directly for phylogenetic inference using neighbour-joining.

*: This program is not to be confused with, and has no relation to, the proprietary trademark and software of Jiwa Financials, North Sydney, Australia.

This software is released under the GNU General Public License v3.0.

Version 1.0 (release July 2014)
The standalone jar file that should work across all operating systems and platforms (.jar) [download]
If you are a programmer, source code (.zip) is available here [download].

Updated January 2015 (.pdf) [download]

If you use jD2Stat and D₂n in your work, please cite:

Chan CX, Bernard G, Poirion O, Hogan JM and Ragan MA (2014)
Inferring phylogenies of evolving sequences without multiple sequence alignment.
Scientific Reports, 4: 6504.
DOI:10.1038/srep06504

Contact
Guillaume Bernard | guillaume.bernard [at] imb.uq.edu.au
Cheong Xin Chan | c.chan [at] imb.uq.edu.au