If you are like me when you first opened up BEAST phylogenetics software, or more specifically BEAUTi GUI, you are immediately impressed but a little overwhelmed by the number of options you have to do reconstruction and phylogenetic analysis more broadly. It’s an amazingly powerful and accessible free software package – particularly with the extra utilities such as Fig Tree and SPREAD (will talk about these in future posts) you really can’t beat BEAST. The tutorials (see below) provide step by step instructions basically mean that anyone can run BEAST. Furthermore, If you have any technical problems, they are often quickly resolved via the google group (https://groups.google.com/forum/#!forum/beast-users).
Despite this, understanding the numerous decisions that have to made throughout the process from sequence alignment to final product is the real challenge here. These decisions can make real differences to the inferences you make so are critical to get right. One weakness in the tutorials is that they tell you how, but don’t give enough detail to why you’d make a particular decision (e.g., why one tree prior over another?). The aims of the following posts will be to demystify this process a little and direct you to useful resources.
The plan is to do this tab by tab of BEAUti and I will assume that you know how to import your data in and set dates/traits (all of this can be learnt from the tutorials easily).
Part 2 – Sites
Part 3 – Clocks
Part 4 – Trees
Part 5 -States, Priors and Operators
Part 6 – Running the whole thing and model selection
In the mean time, if you haven’t already, download BEAST 1.8.4 (http://beast.bio.ed.ac.uk/tutorials) and go through the tutorials: http://beast.bio.ed.ac.uk/tutorials.