PTP on MrBayes output: Tree is neither unrooted nor rooted

[Michelle D]

Hi all, 

I have been trying to conduct PTP and mPTP on a MrBayes Newick tree output. I am recieving the message "Tree is neither unrooted nor rooted" when I try to input a rooted MrBayes tree into both the web-based and command line mPTP program. 

I have tried running MrBayes with the "allcompat" and "halfcompat" commands to form a fully binary tree. I have also tried re-rooting the tree in Geneious and Figtree before exporting as a Newick tree. I have made sure to remove annotations when exporting the Newick file too, but I continue to recieve this message. I was able to run PTP/mPTP succesfully using ML trees. 

Any further suggestions for troubleshooting? Thanks!

Michelle

[Alexandros Stamatakis]

Dear Michelle,

This is probably an issue with the tree format which must be standard
Newick.

Could you please send me the input tree file (to my personal email if
you like).

Alexis

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Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)