arlequin SFS output
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4.7 years ago
decaraa • 0


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!

plink arlequin pgdspider sfs fastsimcoal • 1.7k views
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