What is simuPOP?

simuPOP is a general-purpose individual-based forward-time population genetics simulation environment based on Python, a dynamic object-oriented programming language that has been widely used in biological studies. More specifically,

• simuPOP is a population genetics simulator that simulates the evolution of populations. It uses a discrete generation model although overlapping generations could be simulated using nonrandom mating schemes.
• simuPOP explicitly models populations with individuals who have their own genotype, sex, and auxiliary information such as age. The evolution of a population is modeled by populating an offspring population from parents in the parental population.
• 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.
• simuPOP is a general-purpose simulator that is designed to simulate arbitrary evolutionary processes. 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. In addition, because simuPOP provides a large number of functions to manipulate populations, it can be used as an data manipulatation and analysis tool.

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 (https://github.com/BoPeng/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.