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I'm interested in estimating global FST among several populations of a tetraploid plant species. I'm looking for an R package that can do this, and can preferably also produce an upper and lower bound for a 95% confidence interval for FST. Does anyone know of a package that can be used for this purpose? I'll post a brief overview of my understanding of some of the options, in case I am not understanding something 100% correctly:

The StAMPP package seems really useful for this sort of thing with tetraploid or mixed populations, but unfortunatley it calculates pairwise FST and not a global measure. I'm aware that adegenet can calculate global FST for tetraploid populations, but it doesn't produce the confidence interval, and hierfstat can only be used with haploid or diploid populations. I've also came across the assigner package https://thierrygosselin.github.io/assigner/index.html, but am not sure if this is valid for tetraploid populations.

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  • $\begingroup$ Its an interesting question. I'm skeptical about the value of population specific Fst (global), because it incorporates strong temporal perspective, rather than representing the extant population. Thus its quite different from pairwise Fst. Upvoted. $\endgroup$
    – M__
    May 22 at 2:52
  • $\begingroup$ Personally, I would use adegenet and incorporate resampling with replacement or a simulated replication using your extant data set. This would introduce a confidence interval. It would need some insight into how tetraploid plants interbreed however. $\endgroup$
    – M__
    May 22 at 2:57

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