A while back I posted some messy code to run Phylometa from R, especially useful for processing the output data from Phylometa which is not easily done. The code is still quite messy, but it should work now. I have run the code with tens of different data sets and phylogenies so it should work.
- This new code works with Marc's new version of Phylometa, so please update: http://lajeunesse.myweb.usf.edu/publications.html
Some notes on tree formatting for Phylometa.
1. Trees cannot have node labels - remove them (e.g., tree$node.label < NULL).
2. Trees cannot have zero length branches. This may seem like a non-problem, but it might be for example if you have resolved polytomies and zero length branches are added to resolve the polytomy.
3. I think you cannot have a branch length on the root branch.