Re: [R-sig-phylo] Comparing the topology of two trees

Hi Alastair, See these functions below, dist.topo is in library(Ape) Cheers, John # check for similarity # do the two trees produced by MrBayes and raxML have the same topology? all.equal(tree1, tree2, use.edge.length = FALSE) # result = TRUE or FALSE. # calculate the distance between

Re: [R-sig-phylo] Comparing the topology of two trees

There is also SH.test (Shimodaira-Hasegawa test) in package phangorn And the Icong index by de Vienne which only compares topology (See this website: http://www.ese.u-psud.fr/utilisateurs/devienne/index.html) -Scott On Thursday, March 3, 2011 at 11:37 AM, John Cumbers wrote: Hi Alastair,

Re: [R-sig-phylo] Comparing the topology of two trees

Hi all, To complete this discussion, the package distory computes Billera et al.'s geodesic distance between two trees. Cheers, Emmanuel Scott Chamberlain wrote on 04/03/2011 00:44: There is also SH.test (Shimodaira-Hasegawa test) in package phangorn And the Icong index by de Vienne which

[R-sig-phylo] Comparing the topology of two trees: Summary of responses

Hi All, Thanks very much to everyone for their suggestions! I thought I should summarise the suggestions for one and all: - treedist() and RF.dist() [phangorn] - SteelPenny (1993) - SH.test() [phangorn] - Shimodaira, H.Hasegawa, M. (1999) - dist.topo() [ape] - PennyHendy (1985),

[R-sig-phylo] Comparing the topology of two trees

Good day all, I was wondering if there is a tree statistic that compares the topology of two trees which gives and indication of the degree of similarity or dissimilarity between the trees? Cheers, Alastair ___ R-sig-phylo mailing list