I was looking for a software which gives the Fst p-value and when I analyzed the results obtained with Arlequin, I realized that the Fst values were different than those from Spagedi or Genepop ...
Fst values could be estimated using different methods ( different mathematical equations) . The first one was proposed by Wright (1951), and later came Cockerham (1973) and Weir & Cockerham (1984) ... etc,
sometimes different software use different methods, and thats what you can find out in their manuals ... nevertheless, they all serve the same purpose and can be trusted for your comparisons.