Forward-time Population Genetics Simulations, Methods, Implementation, and Applications, by Bo Peng, Marek Kimmel, and Christopher I Amos
simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease. At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios.
If you are new to simuPOP, please take a look at the Introduction and Features pages and see if this software fits your need. If you have certain evolutionary scenarios in mind, you might want to browse through existing examples and see if one of them happens to fit your need. If you could not find a script that match your need exactly, you can download a script and start from there. The comprehensive simuPOP Documentation will help you along the way.
If you have any question, please feel free to join the simuPOP MailingList and ask.