jmurga/mktest repository overview

⁠ABC-MK

MKtest.jl is a Julia package including a fast Approximate Bayesian Computation version of the McDonald-Kreitman test (ABC-MK) presented in Uricchio et al. (2019)⁠. The new ABC-MK implementation significantly improves the efficiency of the population genetics inferences. Following Uricchio et al.(2019)⁠, the analytical estimations were used to explore the effect of background selection and selective interference on weakly beneficial alleles. Nonetheless, we developed a more straightforward and computationally efficient ABC-based inference procedure that accounts for the DFE of deleterious and beneficial alleles and partial recombination between selected genomic elements. Our approach estimates $\alpha$, $\alpha_W$, $\alpha_S$, and the Gamma distribution DFE parameters.

In addition, the package automatizes other MK-like analyses parsing polymorphic and divergence data as well as including several extensions such as Grapes⁠, aMK⁠, imputedMK⁠ or fwwMK⁠.

See the documentation⁠ for details.