CoaCC simulates a case-control study using a coalescent framework. It assumes a haploid sample of cases and a second haploid sample of controls. Genealogy is generated from these two samples, dependent on the user-specified population history. From this genealogy a distribution of marker-haplotypes is generated by allowing for marker-mutation and recombinations between marker and gene as well as between markers.
The current version is 1.0.1. If you use CoaCC please e-mail firstname.lastname@example.org or fill out the registration form. The software and files can be downloaded here.