msstats_fst
Filed in: C++
A modification of K. Thornton’s msstats program that calculates Weir & Cockerham’s Fst estimator from ms simulations.
msstatsFST.tgz
You must have libsequence installed for this program to function.
To use msstatsFST with Hudson's ms, try this example:
ms 10 1 -t 2 -I 2 6 4 0 -ej 4 2 1 | msstats -I 2 6 4
which will calculate Fst between two simulated populations of size 6 and 4, respectively. It should output two lines of stats, one for each pop. It outputs values of "nan" for all but the final population, which shows the Fst between the two populations. It also works for more than 2 populations, but I cannot remember if the correctness of the calculations for >2 pops has been checked. Please email me for questions or bug reports.