3 \title{Topological Distances Between Two Trees}
5 dist.topo(x, y, method = "PH85")
8 \item{x}{an object of class \code{"phylo"}.}
9 \item{y}{an object of class \code{"phylo"}.}
10 \item{method}{a character string giving the method to be used: either
11 \code{"PH85"}, or \code{"BHV01"}.}
14 This function computes the topological distance between two
15 phylogenetic trees using different methods.
18 a single numeric value.
21 Two methods are available: the one by Penny and Hendy (1985), and the
22 one by Billera et al. (2001).
24 The topological distance is defined as twice the number of internal
25 branches defining different bipartitions of the tips (Penny and Hendy
26 1985). Rzhetsky and Nei (1992) proposed a modification of the original
27 formula to take multifurcations into account.
29 Billera et al. (2001) developed a distance from the geometry of a tree
30 space. The distance between two trees can be seen as the sum of the
31 branch lengths that need be erased to have two similar trees.
34 Billera, L. J., Holmes, S. P. and Vogtmann, K. (2001) Geometry of the
35 space of phylogenetic trees. \emph{Advances in Applied Mathematics},
38 Nei, M. and Kumar, S. (2000) \emph{Molecular evolution and
39 phylogenetics}. Oxford: Oxford University Press.
41 Penny, D. and Hendy, M. D. (1985) The use of tree comparison
42 metrics. \emph{Systemetic Zoology}, \bold{34}, 75--82.
44 Rzhetsky, A. and Nei, M. (1992) A simple method for estimating and
45 testing minimum-evolution trees. \emph{Molecular Biology and
46 Evolution}, \bold{9}, 945--967.
48 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
50 \code{\link{read.tree}} to read tree files in Newick format,
51 \code{\link{cophenetic.phylo}}, \code{\link{prop.part}}
56 dist.topo(ta, ta) # = 0
57 dist.topo(ta, tb) # This is unlikely to be 0 !