Population geneticists have traditionally used Nei's Gst (often confusingly called Fst...) to measure divergence between populations. Recently, it has become clear that simple intereptations of the value of Gst can be misleading. For this reason several new measures differntiation have been developed. mmod is a package that brings some of these measures to R.
The vignette for this package ( avaliable using vignette("demo", package="mmod") from within R) contains an introduction to these methods and and example usage for this package. I strongly suggest new users start by reading this documentation.
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