Generating additional trees

After performing an initial analysis, you may want to sample additional trees. To do so, click on Extend tree building in the Display Window. This will cause a dialog box to appear, which will query for the additional burn-in that is to be performed before new trees are sampled, the number of trees to be sampled and whether to discard the currently saved trees. If you are using this option because the MCMC did not converge in the first chain and you want to run it for more steps to assure convergence, then you should discard the first set of trees. On the other hand, if you want to increase the number of trees that are sampled from the posterior, you may want to keep the trees that are already sampled. The program also provides the option to discard only a subset of the already sampled trees. If that option is selected, trees are deleted in the order that they have been sampled in.

After setting up the tree building, you will be given the option to start the tree building, or to generate job scripts that can be exported to other machines.