Scripts and source files associated with our more recent manuscripts are provided as git repositories on our institutes git server:
CTL fitting: http://git.tuebingen.mpg.de/ctlfit
Coalescence and diversity in sexual populations: http://git.tuebingen.mpg.de/reccoal
Deleterious effects of synonymous mutations in HIV: http://git.tuebingen.mpg.de/synmut
Simulation CTL escape of HIV
Along with the paper "Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses" we provide the source code of a population genetic simulation that allows to efficiently generate artificial data, given model parameters. The program allows the user to specify the population size, recombination rate, mutation rate, and the escape rate of up to 15 CTL escape mutations.
Muller's Ratchet and deleterious mutation selection balance
FFPopSim: An efficient forward simulation package for the evolution of large populations
FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual based simulations, and a complementary one for simulation of the entire genotype distribution. The latter is coded efficiently using Fast-Fourier Transforms to speed up recombination operations. It is available from it project site
Illustrations and tutorials accompanying the review "Genetic Draft, selective interference, and population genetics of rapid adaptation"