Hybridsim: Simulator for generating allele data in isolated populations

We propose a novel two-phase population simulator for generating diploid marker allele data in isolated populations. Our simulator extends Populus, an exact forward-in-time simulator for isolated populations, with a coalescent simulator. The coalescent, while not suitable for completely replacing Populus, is an useful substitute for the over-simpli ed founder generator used in Populus. We believe that this combination makes Hybridsim a very attractive choice for simulating large populations for case-control studies. First in the simulation process a founder population is simulated using an approximated coalescent process with a stepwise and/or in nite sites mutation model in order to establish a realistic genealogy and mutation history for the founders. In the second phase, a separate genealogy and an exact recombination history is generated for the isolate with a discrete generation version of Populus. This enables an accurate simulation of a large population isolate. A dominant mutation disease model can be speci ed into the population afterwards, and nally samples of various types can be obtained for further study. An arbitrary amount of SNP and/or STR markers generated in the coalescence process can be used as markers in the nal allele data. We also discuss some implementation issues and describe our own implementation, which is available for download along with simulated data.