If you have annotated branches in FigTree (for example bootstrap
values, posterior probabilities) then after re-rooting, these may
appear next to the wrong node (i.e., the child of the the node that
was formerly a parent). At the moment, there is not an obvious way to
fix this. I would suggest turning off such labels and then perhaps re-
annotating by hand. Branch lengths and node ages should be correct.
A more obvious point is that node height HPDs and mean values provided
by TreeAnnotator (in the BEAST package) will be meaningless if the
tree is re-rooted.
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624