Finally we will also specify some diffuse “uninformative” but proper priors on the overall molecular clock rate ( from the drop-down menu and using the arrow button, expand the view to reveal the parameters of the Gamma prior.For both the clock rate and the Yule birth rate set the Alpha (shape) parameter to 0.001 and the Beta (scale) parameter to 1000 (Figure 11).The Yule model is a simple model of speciation that is generally more appropriate when considering sequences from different species. You will see a dialog that allows you to define a subset of the taxa in the phylogenetic tree.
So, at this point we will need to link the clock model and tree. Then click on the first drop-down menu in the Clock Model column and rename the shared clock model to ‘clock’. This will make following options and generated log files more easy to read. Then, select the tab since all taxa are from contemporary samples).We leave the Proportion Invariant entry set to zero. This will fix the frequencies to the proportions observed in the data (for each partition individually, once we unlink the site models).This approach means that we can get a good fit to the data without explicitly estimating these parameters.By default each of the gamma shape parameters has an exponential prior distribution with a mean of 1.This implies (see Figure 3.7) we expect some rate variation.