arlequin SFS output

arlequin SFS output



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!







updated 2 hours ago by


written 3.6 years ago by


According to the Arlequin manual ( on pg. 98:

“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.

before adding your answer.

Traffic: 1646 users visited in the last hour

Read more here: Source link