X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fdist.topo.Rd;h=d1542add7b9ac0e1233f11bbba209dd2305ff73f;hb=a2fc961dffe9f9b7994ed880e68c03b2334dc341;hp=3fbedcd0761dc0649bf62775394ecb6a373d9f21;hpb=15e231b55ef0be61c20bfc82efd2316e085122a9;p=ape.git

diff --git a/man/dist.topo.Rd b/man/dist.topo.Rd
index 3fbedcd..d1542ad 100644
--- a/man/dist.topo.Rd
+++ b/man/dist.topo.Rd
@@ -19,7 +19,8 @@ dist.topo(x, y, method = "PH85")
 }
 \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
@@ -33,7 +34,8 @@ dist.topo(x, y, method = "PH85")
   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
@@ -44,8 +46,8 @@ dist.topo(x, y, method = "PH85")
   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.
@@ -54,7 +56,7 @@ dist.topo(x, y, method = "PH85")
   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}}