I've been working with genome-wide data for about 200 samples. I have 150.000 SNPs and I already calculated the Fst using Eigenstrat. I would like to obtain a p-value for each Fst and I tried using Arlequin but it seems to be not able to handle the amount of data. I tried both Windows and Linux versions, without any result. Now I'm working in R with the StAMPP package, and it seems to be working, but the amount of time it requires is huge. Do you have any suggestions? How can I calculate Fst and p-values for my dataset?