https://github.com/cran/ape
Tip revision: 4498162033af49c3fcc98e830182872d87c783fd authored by Emmanuel Paradis on 22 October 2011, 00:00:00 UTC
version 2.8
version 2.8
Tip revision: 4498162
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{"score"}.}
}
\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
branch length score by Kuhner and Felsenstein (1994). The trees are
always considered as unrooted.
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.
The branch length score may be seen as similar to the previous
distance but taking branch lengths into account. Kuhner and
Felsenstein (1994) proposed to calculate the square root of the sum of
the squared differences of the (internal) branch lengths defining
similar bipartitions (or splits) in both trees.
}
\note{
The geodesic distance of Billera et al. (2001) has been disabled: see
the package \pkg{distory} on CRAN.
}
\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.
Kuhner, M. K. and Felsenstein, J. (1994) Simulation comparison of
phylogeny algorithms under equal and unequal evolutionary rates.
\emph{Molecular Biology and Evolution}, \bold{11}, 459--468.
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.
}
\author{Emmanuel Paradis}
\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}