Front Matter


simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. Unlike coalescent-based programs, simuPOP evolves populations forward in time, subject to arbitrary number of genetic and environmental forces such as mutation, recombination, migration and Population/subpopulation size changes. In contrast to competing applications that use command-line options or configuration files to direct the execution of a limited number of predefined evolutionary scenarios, users of simuPOP’s scripting interface could make use of many of its unique features, such as customized chromosome types, arbitrary nonrandom mating schemes, virtual subpopulations, information fields and Python operators, to construct and study almost arbitrarily complex evolutionary scenarios.

simuPOP is provided as a number of Python modules, which consist of a large number of Python objects and functions, including population, mating schemes, operators (objects that manipulate populations) and simulators to coordinate the evolutionary processes. It is the users’ responsibility to write a Python script to glue these pieces together and form a simulation. At a more user-friendly level, an increasing number of functions and scripts contributed by simuPOP users is available in the online simuPOP cookbook. They provide useful functions for different applications (e.g. load and manipulate HapMap samples, import and export files from another application) and allow users who are unfamiliar with simuPOP to perform a large number of simulations ranging from basic population genetics models to generating datasets under complex evolutionary scenarios.

This user’s guide shows you how to install and use simuPOP using a large number of examples. It describes all important concepts and features of simuPOP and demonstrates how to use them in a simuPOP script. Although the new Python 3.x releases are incompatible with Python 2.x, examples in this book are written in a style that is compatible with both versions of Python. For a complete and detailed description about all simuPOP functions and classes, please refer to the simuPOP Reference Manual. All resources, including a pdf version of this guide and a mailing list can be found at the simuPOP homepage

How to cite simuPOP:

Bo Peng and Marek Kimmal (2005) simuPOP: a forward-time population genetics simulation environment. bioinformatics, 21 (18): 3686-3687

Bo Peng and Christopher Amos (2008) Forward-time simulations of nonrandom mating populations using simuPOP. bioinformatics, 24 (11) 1408-1409.