Here's another question. I'm looking for ways to compute distances between two trees when there are differences in the sets of tip labels.
Based on some preliminary tests using simulated trees, phangorn's RF.dist gives me exactly the same results as ape's dist.topo (which makes me wonder if Penny and Hendy (1985)'s topological distance and the Robinson-Foulds distance are equivalent). But, if there is one tip missing from one of the trees, dist.topo gives me a distance anyway, but RF.dist gives me an error message: > tr1<-pbtree(n=30) > tr2<-pbtree(n=29) > dist.topo(tr1, tr2)  51 > RF.dist(tr1, tr2) Error in RF.dist(tr1, tr2) : trees have different labels However, this distance does not seem reasonable to me. For instance, if I take the same tree and drop different tips, I get: > tr<-pbtree(n=10) > tr1<-drop.tip(tr, "t1") > tr2<-drop.tip(tr, "t2") > dist.topo(tr1, tr2)  4 > RF.dist(tr1, tr2) Error in RF.dist(tr1, tr2) : trees have different labels Sometimes dist.topo gives me a distance of 2, other times I get 4, depending on the simulated tree, yet both trees are completely consistent with one another. Is there a metric that would circumvent this issue? Thanks again, Karla [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - Remail@example.com https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://firstname.lastname@example.org/