Re: [R-sig-phylo] similarity of trees
Hi Damien & Scott, I don't know the formula of Icong or MAST, but I'd like to remind you the function prop.part() that finds all the clades in a set of trees and returns the compositions and frequencies, eg: a <- rtree(4) b <- rtree(4) prop.part(c(a, b)) 1: t2 2: t1 3: t3 4: t4 ==> 2 time(s):[1] 1 2 3 4 ==> 1 time(s):[1] 2 3 4 ==> 2 time(s):[1] 2 3 ==> 1 time(s):[1] 1 2 3 This requires the trees to have the same tip labels. It is used in ape by boot.phylo(), and calls a C code. It doesn't seem to be used by other developers though it is certainly efficient and may help in many applications. Emmanuel On Tue, 18 Jan 2011 19:46:30 +0100 "Damien de Vienne" wrote: Dear Scott, Having Icong in R would be nice but it is not the case yet. Sorry... However if someone has a code (in C for example) to compute the maximum agreement subtree (MAST) between two trees, I would be happy to do the rest in order to have the Icong index within R (within the ape package maybe ? And having the simple MAST calculation there would be also very useful I believe). Anyway, if you want to automate the calculation of the Icong index you can still use PAUP* that calculates the MAST and apply afterwards the functions that are in the paper. If you need help, tell me. Damien Le Mar 18 janvier 2011 19:42, Scott Chamberlain a ?crit : Hi Marten, The test I referred to tests for similarity of topology only, ignoring branch lengths. On the website made by de Vienne et al. you can input two newick trees and the site calculates the Icong index, which determines how similar the topologies are, and gives you a p-value. I use it in the context of trying to argue that a tree I have made is *similar enough* to a published tree of the same group of organisms. I believe you have to delete all unshared taxa between the two trees you input. I am interested purely in the trees, not community ecology data, so phylosor and NRI are not applicable in this case. Scott On Tuesday, January 18, 2011 at 12:34 PM, Marten Winter wrote: Dear Scott, do you really want to test for similarity of the shape of the trees? If yes please let me know how to do this :O) If you would also be satisfied with a similarity based on the shared branches I suggest something like Phylosor or may be NRI... cheers, Marten [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org 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
Re: [R-sig-phylo] similarity of trees
Dear Scott, Having Icong in R would be nice but it is not the case yet. Sorry... However if someone has a code (in C for example) to compute the maximum agreement subtree (MAST) between two trees, I would be happy to do the rest in order to have the Icong index within R (within the ape package maybe ? And having the simple MAST calculation there would be also very useful I believe). Anyway, if you want to automate the calculation of the Icong index you can still use PAUP* that calculates the MAST and apply afterwards the functions that are in the paper. If you need help, tell me. Damien Le Mar 18 janvier 2011 19:42, Scott Chamberlain a écrit : > Hi Marten, > > > > The test I referred to tests for similarity of topology only, ignoring > branch lengths. On the website made by de Vienne et al. you can input two > newick trees and the site calculates the Icong index, which determines > how similar the topologies are, and gives you a p-value. I use it in the > context of trying to argue that a tree I have made is *similar enough* to > a published tree of the same group of organisms. I believe you have to > delete all unshared taxa between the two trees you input. > > > I am interested purely in the trees, not community ecology data, so > phylosor and NRI are not applicable in this case. > > > Scott > On Tuesday, January 18, 2011 at 12:34 PM, Marten Winter wrote: > > >> Dear Scott, >> >> >> do you really want to test for similarity of the shape of the trees? If >> yes please let me know how to do this :O) >> >> If you would also be satisfied with a similarity based on the shared >> branches I suggest something like Phylosor or may be NRI... >> >> cheers, Marten >> >> >> > > > > > > [[alternative HTML version deleted]] > > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > 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
Re: [R-sig-phylo] similarity of trees
Hi Marten, The test I referred to tests for similarity of topology only, ignoring branch lengths. On the website made by de Vienne et al. you can input two newick trees and the site calculates the Icong index, which determines how similar the topologies are, and gives you a p-value. I use it in the context of trying to argue that a tree I have made is *similar enough* to a published tree of the same group of organisms. I believe you have to delete all unshared taxa between the two trees you input. I am interested purely in the trees, not community ecology data, so phylosor and NRI are not applicable in this case. Scott On Tuesday, January 18, 2011 at 12:34 PM, Marten Winter wrote: > Dear Scott, > > do you really want to test for similarity of the shape of the trees? If yes > please let me know how to do this :O) > > If you would also be satisfied with a similarity based on the shared branches > I suggest something like Phylosor or may be NRI... > > cheers, > Marten > > [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
