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{"score"}.}
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 branch length score by Kuhner and Felsenstein (1994). The trees are
23 always considered as unrooted.
25 The topological distance is defined as twice the number of internal
26 branches defining different bipartitions of the tips (Penny and Hendy
27 1985). Rzhetsky and Nei (1992) proposed a modification of the original
28 formula to take multifurcations into account.
30 The branch length score may be seen as similar to the previous
31 distance but taking branch lengths into account. Kuhner and
32 Felsenstein (1994) proposed to calculate the square root of the sum of
33 the squared differences of the (internal) branch lengths defining
34 similar bipartitions (or splits) in both trees.
37 The geodesic distance of Billera et al. (2001) has been disabled.
40 Billera, L. J., Holmes, S. P. and Vogtmann, K. (2001) Geometry of the
41 space of phylogenetic trees. \emph{Advances in Applied Mathematics},
44 Kuhner, M. K. and Felsenstein, J. (1994) Simulation comparison of
45 phylogeny algorithms under equal and unequal evolutionary rates.
46 \emph{Molecular Biology and Evolution}, \bold{11}, 459--468.
48 Nei, M. and Kumar, S. (2000) \emph{Molecular evolution and
49 phylogenetics}. Oxford: Oxford University Press.
51 Penny, D. and Hendy, M. D. (1985) The use of tree comparison
52 metrics. \emph{Systemetic Zoology}, \bold{34}, 75--82.
54 Rzhetsky, A. and Nei, M. (1992) A simple method for estimating and
55 testing minimum-evolution trees. \emph{Molecular Biology and
56 Evolution}, \bold{9}, 945--967.
58 \author{Emmanuel Paradis}
60 \code{\link{read.tree}} to read tree files in Newick format,
61 \code{\link{cophenetic.phylo}}, \code{\link{prop.part}}
66 dist.topo(ta, ta) # = 0
67 dist.topo(ta, tb) # This is unlikely to be 0 !