CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models.
CoaSim effectively constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP, micro-satellite, and other haplotypes/genotypes.
The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.
CoaSim is developed in collaboration between Bioinformatics ApS and Bioinformatics Research Center (BiRC).
CoaSim is written in C++ and Guile Scheme and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM files. The source code has been successfully compiled on various Linux and UNIX systems, under OS X and under Windows with Cygwin.
As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.
What's New in This Release:
· Callbacks for population structure events (bottlenecks, migration, etc.) have been added.
· A major bug that caused the starting and ending times of epochs to be wrong in some cases (starting too late or never terminating) has been fixed.