prfreq

Uses Poisson random fields to calculate expected allele frequency distributions under various possible distributions of selective effects and demographic models. prfreq estimates demography and a constant selection coefficient to allow for inference of the distribution of fitness effects (DFE) of newly arising mutations. This maximum likelihood approach uses putatively neutral synonymous Single Nucleotide Polymorphisms (SNPs) to infer the demographic history of the population and then numerically solves for the transient distribution of allele frequencies for a given selective effect under that demographic model.