X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fnj.Rd;h=88d2258c5893c5da384b74136ac357635d4b66d9;hb=1ad48c7a70983375138a6500372db588c8a3a134;hp=3b8cb64c531f690db46b2d308f0062a6f96d8353;hpb=fe18d99e0a288498b3c52391045c1f154887d085;p=ape.git

diff --git a/man/nj.Rd b/man/nj.Rd
index 3b8cb64..88d2258 100644
--- a/man/nj.Rd
+++ b/man/nj.Rd
@@ -18,11 +18,15 @@ nj(X)
   Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new
   method for reconstructing phylogenetic trees. \emph{Molecular Biology
     and Evolution}, \bold{4}, 406--425.
+
+  Studier, J. A. and Keppler, K. J. (1988) A note on the
+  neighbor-joining algorithm of Saitou and Nei. \emph{Molecular Biology
+    and Evolution}, \bold{5}, 729--731.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link{write.tree}}, \code{\link{read.tree}},
-  \code{\link{dist.dna}}, \code{\link{mlphylo}}, \code{\link{bionj}},
+  \code{\link{dist.dna}}, \code{\link{bionj}},
   \code{\link{fastme}}
 }
 \examples{
@@ -31,9 +35,10 @@ x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
        10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
        5, 6, 10, 9, 13, 8)
 M <- matrix(0, 8, 8)
-M[row(M) > col(M)] <- x
-M[row(M) < col(M)] <- x
-rownames(M) <- colnames(M) <- 1:8
+M[lower.tri(M)] <- x
+M <- t(M)
+M[lower.tri(M)] <- x
+dimnames(M) <- list(1:8, 1:8)
 tr <- nj(M)
 plot(tr, "u")
 ### a less theoretical example