When I was using fsc to simulate my data, I struggled with whether to use monomorphic sites for simulation. I see that you used the -0 parameter when running fsc(https://speciationgenomics.github.io/fastsimcoal2/), but I read the fsc documentation saying that you need to fix the parameters on the .est file when using the -0 parameter, and I went to see your est file and did not find the specified parameter(https://github.com/speciationgenomics/data/blob/master/diff_geneflow.est). Can you please tell me why?
Hello,
When I was using fsc to simulate my data, I struggled with whether to use monomorphic sites for simulation. I see that you used the -0 parameter when running fsc(https://speciationgenomics.github.io/fastsimcoal2/), but I read the fsc documentation saying that you need to fix the parameters on the .est file when using the -0 parameter, and I went to see your est file and did not find the specified parameter(https://github.com/speciationgenomics/data/blob/master/diff_geneflow.est). Can you please tell me why?
Thank you.
Best wishes!