I found the java software package TreeCmp to be very good with the pruning function implemented:
Bogdanowicz, Damian, Krzysztof Giaro, and Borys Wróbel. “TreeCmp: Comparison of Trees in Polynomial Time.” *Evolutionary Bioinformatics Online* 8 (2012): 475–87. Chris Buddenhagen cbuddenha...@gmail.com On Fri, Nov 25, 2016 at 6:00 AM, <r-sig-phylo-requ...@r-project.org> wrote: > Send R-sig-phylo mailing list submissions to > r-sig-phylo@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > or, via email, send a message with subject or body 'help' to > r-sig-phylo-requ...@r-project.org > > You can reach the person managing the list at > r-sig-phylo-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-phylo digest..." > > > Today's Topics: > > 1. Re: distances between trees (Emmanuel Paradis) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 24 Nov 2016 18:36:37 +0100 > From: Emmanuel Paradis <emmanuel.para...@ird.fr> > To: Karla Shikev <karlashi...@gmail.com>, r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] distances between trees > Message-ID: <8de184e7-3aba-2c32-42b2-54d5263bd...@ird.fr> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hi Karla, > > I cannot answer to your question on comparing trees with different sets > of labels, but surely dist.topo() should return an error in this > situation. I modified the code to handle this -- it is also much faster > (~ 100 times faster when comparing 100 trees with 100 tips). > > And yes, you are right: from the definition of the RF distance in > ?RF.dist and the one for the PH distance in ?dist.topo, they are the same. > > Best, > > Emmanuel > > Le 20/11/2016 ? 18:07, Karla Shikev a ?crit : > > 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) > > [1] 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) > > [1] 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 - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > > > > > > Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : > http://f.security-mail.net/301GGR55Htk > > > > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > ------------------------------ > > End of R-sig-phylo Digest, Vol 106, Issue 15 > ******************************************** > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/