[R-sig-phylo] Measures of dissimilarity between phylogenetic trees

Liam J. Revell liam.revell at umb.edu
Tue Dec 27 01:06:42 CET 2011

Hi Bruno.

RF.dist in the phangorn package computes Robinson-Foulds distance 
(http://en.wikipedia.org/wiki/Robinson-Foulds_metric). This is not 
obvious, but (unless you want the position of the root to affect the 
score) you should probably unroot your trees before using RF.dist, e.g.:
 > tr1<-read.tree(text="(A,(B,C));")
 > plot(tr1)
 > tr2<-read.tree(text="((A,B),C);")
 > # tr1 & tr2 have the same unrooted topology, yet:
 > RF.dist(tr1,tr2)
[1] 2
 > RF.dist(unroot(tr1),unroot(tr2))
[1] 0

In addition, phangorn:treedist and ape:dist.topo provide other metrics 
of tree distance.

All the best, Liam

Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.revell at umb.edu
blog: http://phytools.blogspot.com

On 12/26/2011 6:27 PM, Bruno de Medeiros wrote:
> Hi everyone,
> I am simulating characters evolving in a phylogetic tree under a number of
> models and using those characters to build another tree using parsimony.
> I would like, then, to measure how similar are the recovered trees when
> compared to the original ones, taking only topology into account. Is there
> any function in the R packages to calculate tree distance metrics? I
> considered using TNT (the program that I am using to build phylogenies) to
> calculate SPR distances, but it would be much more convenient if there were
> a way of doing it in R.
> Thanks in advance,
> Bruno
> --
> Bruno A. S. de Medeiros
> PhD Student - Farrell Lab
> Harvard University
> 	[[alternative HTML version deleted]]
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