dist.topo

0th

Percentile

Topological Distances Between Two Trees

This function computes the topological distance between two phylogenetic trees using different methods.

Keywords
manip
Usage
dist.topo(x, y, method = "PH85")
Arguments
x
an object of class "phylo".
y
an object of class "phylo".
method
a character string giving the method to be used: either "PH85", or "BHV01".
Details

Two methods are available: the one by Penny and Hendy (1985), and the one by Billera et al. (2001).

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 two similar trees.

Value

  • a single numeric value.

References

Billera, L. J., Holmes, S. P. and Vogtmann, K. (2001) Geometry of the space of phylogenetic trees. Advances in Applied Mathematics, 27, 733--767.

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.

See Also

read.tree to read tree files in Newick format, cophenetic.phylo, prop.part

Aliases
  • dist.topo
Examples
ta <- rtree(30)
tb <- rtree(30)
dist.topo(ta, ta) # = 0
dist.topo(ta, tb) # This is unlikely to be 0 !
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

Community examples

shivanis270@gmail.com at Dec 3, 2019 ape v3.0-9

dist.topo(tree1, tree2, method = "PH85")