DEEGEP is a simple statistical method for testing for natural selection from a high dimensional (i.e. multiple population) allele frequency spectrum. The method uses a neutral control defined by the user (e.g. intergenic sites) to learn a background neutral distribution. This is accomplished by approximating the density with a finite expansion of Gegenbauer polynomials, inspired by Kimura’s classic result in theoretical population genetics. One can then test for natural selection on a second set of putatively functional sites (e.g. microRNAs) by comparing the multi-population allele frequency spectrum to the neutral control.
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