If you publish work using results from CubeX, please cite our 2007 BMC Bioinformatics paper (see below).

Please enter valid positive integers in all 9 cells.
11 12 22
SNP 1 11


This program calculates haplotype frequencies using the exact solution to the cubic equation rather than an iterative approach.
Please enter the observed diplotype numbers in the cells of the table above, then click submit to analyse. Values should be positive integers.

CubeX for batch use

Click here to download a version of CubeX (Python script) for batch use. This takes diplotype inputs from text file (one SNP pair per line) and exports xml.

Copyright and Licence

This program is copyright (2006-7). Use is free under the terms of the CubeX licence, but no liability is accepted for any costs or errors incurred by use of the software. Any use of the program should be cited in publications: 

Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'
Tom R Gaunt, Santiago Rodriguez, Ian NM Day
BMC Bioinformatics 2007, 8:428 (2 November 2007)

Any user wishing to obtain the code for their own use should contact cubex@oege.org