Note about re-rooting in FigTree

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Andrew Rambaut

Feb 21, 2008, 6:30:59 AM2/21/08
This is a note of caution about re-rooting trees in FigTree.

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.


Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - TEL - +44 131 6508624

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