Dear BioStars community:
I would like to know if there is a software or script that calculates Hudson's Fst estimator (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1205159/) at both Population and SNP level, the first to asses genetic distance between population and the second to detect highly divergent SNPs. I have used the EIGENSOFT software but this only produces Fst values at population level (pairwise matrix), but not for single SNPs. I also have used the well known method from Weir and Cockerham implemented in PLINK, but Bhatia et al, 2013 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759727/#B16) recommends to use Hudson's estimator because it behaves better with uneven population sizes.
Thanks in advance.