I’ve converted a ped file to arlequin using pgdspider. As I don’t have the ancestral state, I haven’t done the numeric conversion. Yet, when I ask arlequin to output the SFS, it returns MAF files, i.e., theoretically, the folded SFS. When I look into this folded SFS, they don’t seem folded at all, as for a sample of 5 individuals, I get
“Note that both derived and minor allele SFS are produced in all cases, even if the ancestral state is not known
for sure. It is the responsibility of the user the correct file for demographic inference.”
So you should get both an unfolded SFS and a folded SFS. But if you don’t have the ancestral states determined (as with an outgroup), you should not use the outputted folded SFS.