Tutorial 4: Questions - BEAST2-Dev/codonsubstmodels GitHub Wiki

What are the different assumptions made considering the four types of equilibrium codon frequencies π_j, such as "equal", "F1X4", "F3X4", and "F60/F61"?

What parameter in M0 tells us the selective forces acting on proteins? And how is its value related to the relative rates of synonymous and nonsynonymous substitutions?

Do we (humans) have strong evolutionary pressure regarding to the given protein-coding sequences from this analysis?