Dear community members,
I'm trying out STACEY for the first time, and having trouble with the convergence. I'm using two genes (mitochondrial and nuclear), 65 taxa, Optimised Relaxed Clock for both genes, at 20000000 Chain length.
There are 10 parameters with ESS not converging. Prior, NClusters, and BirthDeathCollapse are the lowest, and it doesn't seem they would converge with longer chain length.
Any help will be appreciated!
Jeong