How do I tell BEAST to use an outgroup?
The simple answer is that you may not want to – BEAST will sample the root position along with the rest of the nodes in the tree. If you then calculate the proportion of trees that have a particular root, you obtain a posterior probability for this root position. However if you have a strong prior for an outgroup then you can constrain the ingroup to be monophyletic. See this tutorial for details of how to do this.
