Does anybody know why Arlequin (2.001) won't calculate conventional Fst and
AMOVA for microsatellite data (or any other) in which the gametic phase is
unknown? It doesn't seem to make any sense to say that gametic phase is
known for 2 or more loci that are unlinked, which is usually the case for
microsatellites. Is this a quirk of the software or is there a theoretical
reason for it?
nb. I am using version 2.001 and even tried it with the data on page 38 of