By Peter Unmack
In BEAST, trying to create a user supplied tree topology with branch lengths that are compatible with various age constraints you have set in BEAST can be difficult to say the least. There are options available to try and get around this. One is to run r8s, another is to use TreeEdit.
TreeEdit is a bit quirky, but it was written a long time ago. It is only available for Macs and can be downloaded from http://tree.bio.ed.ac.uk/software/treeedit/. Take your file on the Mac and set it so that the default program to open the file with is TreeEdit (TreeEdit had issues with recognizing my files as being the right type that could be opened on the Mac I was using). Double click it to open it. Newick or nexus trees are ok. First make the tree ultrametric (use NPRS). Then multiply the branches by a set amount, you can view the branch lengths in FigTree, add the scale at the bottom (reverse it) to make it easier to check. Keep fiddling until you get the right length for the node in question.
Export the tree file. Click off all the translation table stuff. Now you can either add it to your nexus file when you import your data into BEAUti, or manually insert the tree into your xml file.
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