For simplicity, let’s set the clock first; we will discuss these distributions a little later.
In BEAST, we input the mutation rate using the ‘clock.rate’ parameter, which is in units of substitutions/site/unit time (default). If you leave the parameter set to 1.0 and do not check “estimate,” then you are going to get a resulting phylogeny or demographic model with units of substitutions/site, the same as if you were just reconstructing a phylogeny using standard maximum likelihood or Bayesian inference analysis methods.
When we talk about divergence as a percentage, x% pairwise divergence between two lineages is equivalent to x%/2 divergence per lineage (along one branch of a two-tip phylogenetic tree). fix it) to exactly this rate (taking it as a mean rate across the phylogeny of your samples)…
Next, click on the “Clocks” tab (this applies to BEAUti 1.7.4; older versions of this software may have a tab named “Clock Models”). Importantly, clock rates if constant can be spread across a range of values (e.g.
uniform prior); however, a constant mutation rate is not necessary, and mutation can be modeled using several distributions.
You can get the latest version at the BEAST website, which can be accessed by clicking here [ or you can download BEAST2 here].
I’d also point out that BEAST developers have provided a very useful set of tutorials as well as a frequently-visited google group for discussing and dealing with issues related to BEAST analysis.