DFE-alpha

DFE-alpha was initially written to estimate the distribution of fitness effects (DFE) of new deleterious mutations using within-species nucleotide polymorphism data. It was subsequently extended to estimate the rate of adaptive molecular evolution, and then to infer the rate and fitness effects of advantageous mutations. The DFE is estimated by maximum likelihood (ML) based on site frequency spectra (SFSs) for two sets of nucleotide sites, one set assumed to be subject to mutation, selection and genetic drift and the other set of sites assumed to be evolving neutrally. The DFE is assumed to be a gamma distribution with shape parameter beta (β), or a model in which all mutations have equal effects can be run. The mean mutational effect is estimated on a scale Nes, where Ne is a measure of the recent effective population size and s is the selection strength acting on a new mutation.