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:

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>    1. Re: distances between trees (Emmanuel Paradis)
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> ----------------------------------------------------------------------
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> 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]]
> >
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