The forward simulation code is a tool to model evolution of a population under the Wright-Fisher model. The code incorporates population expansion, bottleneck, speciation and migration. Several selection and fitness mechanisms are available: selective sweeps, foreground selection in one region with a distinct background selection in neighboring regions, epistasis, and truncation selection. The code is implemented in the C++ programming language.
The project was developed by Victor Spirin in Shamil Sunyaev's lab at Brigham and Women's Hospital/Harvard Medical School.
Downloads, documentation, wiki pages are available on the souceforge project page.
Acknowledgements
Special thanks to Tobias Lenz and to Adam Kiezun for help with testing and debugging the code and many helpful suggestions during the code design and development.Reference
Tobias L. Lenz, Victor Spirin, Daniel M. Jordan & Shamil R. Sunyaev (In preparation). Excess of deleterious mutations around HLA immune genes reveals evolutionary cost of balancing selection.