I have a question about the input obs.file for the fastsimcoal simulation. What is the difference when you using the folded and unfolded SFS in fastsimcoal? When I prepare the SFS input file in Arlequnin, I have vcf file bue the ancestral state is not knowen, I only got the MAF.obs output. But from the Arlequin manual said the both derived and minor allele SFS are produced in all cases, even if the ancestral state is not known. So I don't know the problem is? I am appreciate if anyone could answer my question, I am stuck here.
Thank you very much!