https://github.com/cran/ape
Tip revision: b2e768879a4de1e6742930fa884ac9578bc3d930 authored by Emmanuel Paradis on 19 November 2006, 00:00:00 UTC
version 1.9
version 1.9
Tip revision: b2e7688
dist.topo.Rd
\name{dist.topo}
\alias{dist.topo}
\title{Topological Distances Between Two Trees}
\usage{
dist.topo(x, y, method = "PH85")
}
\arguments{
\item{x}{an object of class \code{"phylo"}.}
\item{y}{an object of class \code{"phylo"}.}
\item{method}{a character string giving the method to be used: either
\code{"PH85"}, or \code{"BHV01"}.}
}
\description{
This function computes the topological distance between two
phylogenetic trees using different methods.
}
\value{
a single numeric value.
}
\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.
}
\author{
Emmanuel Paradis \email{paradis@isem.univ-montp2.fr}
}
\references{
Billera, L. J., Holmes, S. P. and Vogtmann, K. (2001) Geometry of the
space of phylogenetic trees. \emph{Advances in Applied Mathematics},
\bold{27}, 733--767.
Nei, M. and Kumar, S. (2000) \emph{Molecular evolution and
phylogenetics}. Oxford: Oxford University Press.
Penny, D. and Hendy, M. D. (1985) The use of tree comparison
metrics. \emph{Systemetic Zoology}, \bold{34}, 75--82.
Rzhetsky, A. and Nei, M. (1992) A simple method for estimating and
testing minimum-evolution trees. \emph{Molecular Biology and
Evolution}, \bold{9}, 945--967.
}
\seealso{
\code{\link{read.tree}} to read tree files in Newick format,
\code{\link{cophenetic.phylo}}, \code{\link{prop.part}}
}
\examples{
ta <- rtree(30)
tb <- rtree(30)
dist.topo(ta, ta) # = 0
dist.topo(ta, tb) # This is unlikely to be 0 !
}
\keyword{manip}