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]

Citing jD2Stat

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.

Guillaume Bernard | guillaume.bernard [at]
Cheong Xin Chan | c.chan [at]

©2013-15 Cheong Xin Chan, Guillaume Bernard and Mark Ragan. Information on this site does not relate to the official business of any institutions at The University of Queensland and shall be understood as neither given nor endorsed by any of the forementioned.