Detects gene-gene interactions from case-control haplotype data. Complex diseases involve multiple genes with low penetration which may be distributed over the genome. Most of the current haplotype association methods are typically restricted in length and consist of alleles from contiguous SNPs. These approaches have limited capacity to detect epistasis from multiple gene-gene interactions.

Recent evidence has shown that the 3-D structure of chromosomes can play a role in allowing SNPs to interact with genetic elements which are physically separated by great distances. We hypothesize that interactions between different chromosomes may play a role in disease susceptibility.

Thus we have developed a cooperative coevolutionary algorithm (CCA) to detect gene-gene interactions from case-control haplotype data; moreover, this algorithm can tolerate up to 15% missing/ambiguous positions in haplotype data arising during haplotype phasing from genotypes. Further, the algorithm can compute epistatic associations from genes spanning multiple chromosomes.

Requirements:
* Java

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