Hello,
I am working on a 29 plant species data set. I run a codon model test in datamonkey and use the batch file to calculate the final tree in HyPhy. The codon data (nexus) file contains a tree topology which is to be used. However, the tree topology is changed in the final tree. In detail, the root taxon is placed in another cluster. This is frustrating because I want to map characters on the final tree and the main interest is on the reconstructed character state at the root of the tree. The message log tells me that the batchfile (or a procedure called therein) used RerootTree. Is there a way to disable RerootTree in the batchfile? I tried already RerootTree = 0 but got an error message.
Many thanks for your help,
Markus

That works. I realised that the batchfile from datamonkey calls the batchfile AnalyseCodonData.bf. I disabeled Do_Tree_Rebalance and now the analysis does not anymore "destroy" my topology.
Many thanks,
Markus

Hi,
I see the rationale behind the rerooting procedure. But if the users inludes a tree (topology) he most likely wants the program to stick to it.? Wouldn't it be useful to automatically disable the rebalance procedure if the codon data file includes a tree? Or would this dramatically increase computation time in some cases (this was not the case with my data)?
Cheers,
Markus