some updates for ape 3.0-6

[ape.git] / man / seg.sites.Rd

diff --git a/man/seg.sites.Rd b/man/seg.sites.Rd
index 19efd2b1b31d7d51da2b0034ad21f2dd75894823..81f046ae9d57fa331192dafb901f5d35a5c32975 100644 (file)
--- a/man/seg.sites.Rd
+++ b/man/seg.sites.Rd
@@ -15,20 +15,21 @@ seg.sites(x)
 }
 \details{
   If the sequences are in a list, all the sequences must be of the same
-  length.
+  length. Ambiguous nucleotides are ignored.
 }
 \value{
-  A numeric vector giving the indices of the segregating sites.
+  A numeric (integer) vector giving the indices of the segregating
+  sites.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \note{
   The present version looks for the sites which are ``variable'' in the
   data in terms of different \emph{letters}. This may give unexpected
   results if there are ambiguous bases in the data.
 }
 \seealso{
-  \code{\link{base.freq}}, \code{\link{GC.content}},
-  \code{\link{theta.s}}, \code{\link{nuc.div}}
+  \code{\link{base.freq}}, \code{\link[pegas]{theta.s}},
+  \code{\link[pegas]{nuc.div}}
 }
 \examples{
 data(woodmouse)