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
1 observation d0_0 d0_1 d0_2 d0_3 d0_4 d0_5 d0_6 d0_7 d0_8 d0_9 d0_10 5761 995.5 744.5 673.5 551.5 520 492.5 394.5 357.5 327.5 751
I cannot get easySFS to work on my mac or my linux box nor angsd... so Arlequin was my only hope other than coding the SFS myself - including a joint 6D SFS...
So what's this output that Arlequin gives me and how to get a folded SFS from a ped file?
Many thanks for your help!