I was wondering if anyone knows of an R package that can calculate population specific Fst (sensu Weir and Hill 2002)?

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J. Patrick Kelley

Package "pegas":

http://bioinformatics.oxfordjournals.org/content/26/3/419.full

http://cran.r-project.org/web/packages/pegas/pegas.pdf

Philippe Henry

Cool, thanks Patrick! I ended up using hierfstat (http://www2.unil.ch/popgen/softwares/hierfstat.htm), more specifically the betai function which calculates some Fst coefficients from Weir and Hill (2002).