tr1 and the second column contains the matching nodes from tr2, inasmuch as they can be identified. For method="descendants", pairs of matching nodes are defined by sharing all descendant leaves in common. for method="distances", nodes are considered to matched if the share the same set of distances (or proportional distances, for optional argument corr=TRUE) to all tips.matchNodes(tr1, tr2, method=c("descendants","distances"), ...)"descendants" uses the tip species descended from each node; "distances" uses the distances from the nodes to the tips. Any umambiguous shortening of "descendants" or method. tol is a tolerance value for the difference from exact matching that is allowed for method="distances". corr, which is FALSEtr1 with the second column containing matching nodes in tr2, with the criterion for matching defined by method.fastAnc.