}
\details{
Two methods are available: the one by Penny and Hendy (1985), and the
- branch length score by Kuhner and Felsenstein (1994).
+ 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
similar bipartitions (or splits) in both trees.
}
\note{
- The geodesic distance of Billera et al. (2001) has been disabled.
+ 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
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.
+ 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.
testing minimum-evolution trees. \emph{Molecular Biology and
Evolution}, \bold{9}, 945--967.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{read.tree}} to read tree files in Newick format,
\code{\link{cophenetic.phylo}}, \code{\link{prop.part}}