[R-sig-phylo] Measures of dissimilarity between phylogenetic trees
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
Re: [R-sig-phylo] Measures of dissimilarity between phylogenetic trees
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.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 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Measures of dissimilarity between phylogenetic trees
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_metrichttp://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-phylohttps://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
