Tree comparison. Two trees are compared in order to identify those nodes that have the same branching orders within subtree rotation (white). If a progressive alignment has been created using to the old tree, then alignments at these nodes can be retained as the same result would be produced at those nodes by the new tree. New alignments are needed at the changed (black) nodes only.
Edgar BMC Bioinformatics 2004 5:113 doi:10.1186/1471-2105-5-113