Hi,

I am running BAMM on different Newick-format chronograms. While all other trees run perfectly fine, I am getting some strange results when using one particular tree. This tree originally had a polytomy, which I could not resolve using the multi2di function in R, so I changed branch lengths in the raw text file. Because I could not change branch lengths manually and maintain the tree perfectly ultrametric, I then used the force.ultrametric function to fix it. However, I do not think this is the source of my problem, because the results are off all across the tree, not just in the clade I modified.

Once I run BAMM, the analysis itself is much much slower than it is with my other, much bigger trees (for control file and run info see attachments). The resulting event.data file is huge (65MB) and the plot.bammdata visuals are a mess (see attachments Result1 and Result3). It looks to me as if it does not recognise branches and/or nodes correctly, so it plots rate shifts on branches instead of nodes and, for some reason, plots hundreds of them.

If anyone has seen anything like this before I would greatly appreciate your help. If you need any additional information please contact me. Thanks in advance,

Eva Turk