This is a custom version of Parallel PopGen Package (3P) v0.3.2 combined with the ability to ouput SFS for mutation-selection equilibirum models. The main repository can be found here: https://github.com/DL42/ParallelPopGen. It was created for the selection at synonymous sites in Drosophila paper: https://www.biorxiv.org/content/10.1101/106476v2. The simulation programs referenced in the paper can be found in folders project/simulation and project/expectation.
A third program project/likelihood estimates categorical DFE & pseudo-demographic parameters using maximum-likelihood for site frequency spectra in a python interface. It is a GPU-accelerated, python version of the Matlab program used in the paper https://github.com/DL42/SFS_DFE_categorical. However, it was not used for the synonymous sites paper. If you wish to use it in your own work, please cite the GO Fish paper:
Accelerating Wright–Fisher Forward Simulations on the Graphics Processing Unit David S. Lawrie G3: GENES, GENOMES, GENETICS September 1, 2017 vol. 7 no. 9 3229-3236; https://doi.org/10.1534/g3.117.300103