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The analysis of the evolutionary dynamics of a population with manypolymorphic loci is challenging since a large number of possible genotypesneeds to be tracked. In the absence of analytical solutions, forward computersimulations are an important tool in multi-locus population genetics. The runtime of standard algorithms to simulate sexual populations increases as 8^Lwith the number L of loci, or with the square of the population size N. We havedeveloped algorithms that allow to simulate large populations with a run-timethat scales as 3^L. The algorithm is based on an analog of the Fast-FourierTransform (FFT) and allows for arbitrary fitness functions (i.e. any epistasis)and genetic maps. The algorithm is implemented as a collection of C++ classesand a Python interface.

FFPopSim: An efficient forward simulation package for the evolution of large populations