dist.topo(x, y, method = "PH85")
"phylo"
."phylo"
."PH85"
, or "BHV01"
.The topological distance is defined as twice the number of internal branches defining different bipartitions of the tips (Penny and Hendy 1985). Rzhetsky and Nei (1992) proposed a modification of the original formula to take multifurcations into account.
Billera et al. (2001) developed a distance from the geometry of a tree space. The distance between two trees can be seen as the sum of the branch lengths that need be erased to have to similar trees.
Nei, M. and Kumar, S. (2000) Molecular evolution and phylogenetics. Oxford: Oxford University Press.
Penny, D. and Hendy, M. D. (1985) The use of tree comparison metrics. Systemetic Zoology, 34, 75--82.
Rzhetsky, A. and Nei, M. (1992) A simple method for estimating and testing minimum-evolution trees. Molecular Biology and Evolution, 9, 945--967.
read.tree
to read tree files in Newick format,
dist.phylo
, prop.part
ta <- rtree(30)
tb <- rtree(30)
dist.topo(ta, ta) # = 0
dist.topo(ta, tb) # This is unlikely to be 0 !
Run the code above in your browser using DataLab