Hi Liam, Many thanks.
Just an additional question related to Robinson-Foulds distance. It seems RF.dist() requires the compared trees to be binary. Is there any standard procedure for dealing with multifurcating trees? Best, Bruno -- Bruno A. S. de Medeiros PhD Student - Farrell Lab Harvard University 2011/12/26 Liam J. Revell <liam.rev...@umb.edu> > Hi Bruno. > > RF.dist in the phangorn package computes Robinson-Foulds distance ( > http://en.wikipedia.org/wiki/**Robinson-Foulds_metric<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/<http://faculty.umb.edu/liam.revell/> > email: liam.rev...@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]] >> >> ______________________________**_________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/r-sig-phylo<https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
