How to use bModelTest

There are two ways you can use bModelTest

• by model selection: first run an analysis with bModelTest and select the model that has most posterior support. Run the final analysis with the site model (say HKY + 4G + estimated frequencies, see details below) that has most posterior support.

• by model averaging: you just run the analysis with bModelTest as site model and the BEAST analysis averages over all models, and use this as you analysis.

The latter is recommended, since it averages out uncertainty over models, and if there is much uncertainty about the model committing to a single model may bias estimates. Furthermore, model averaging requires less computational effort, since you don't have to run the "model selection" analysis separate from the full analysis.

Setting up a (non-standard) substitution model in BEAUti

Some, but not all of the 203 reversible models, are supported by BEAUti. If the model you want is supported (e.g. HKY, TN93, GTR) just select it from the drop down box in the site model panel.

If it is not supported, e.g. TPM2 (model 121323), select GTR as substitution model. Then, select the menu Mode/Allow parameter linking and a link icon appears next to the rates of GTR. If you click the icon, a list of parameters pops up that you can link with. To create a TPM2 model, you just link AC with AT, CG with GT and AG with CT. By default, CT is fixed at 1, so linking AG with CT causes AG to be fixed to 1 as well. If you would estimate them they would not be identifiable with tree height and clock rate, so you want at least one of the parameters to be fixed (i.e. not estimated). You can leave the other rates to be estimated.

Setting up a frequency model in BEAUti

In the site model panel, for equal frequencies, select ‘All equal’ from the drop down menu with label 'frequencies'. For unequal frequencies, make sure to keep them at ‘estimated’.

Setting up a gamma site heterogeneity in BEAUti

For no gamma rate heterogeneity, set gamma category count to 1 (or less). If you want to use gamma rate heterogeneity, set gamma category count to 4, and select the ‘estimate’ box next to the shape parameter.

Setting up proportion invariable in BEAUti

For no proportion invariable, set the associated entry in the site model panel to 0 and keep the estimate box unchecked. If you want to have a proportion invariable, set the associated entry to a small value (say 0.1) and make sure the estimate box is checked.