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diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd
index f0a650b..8ac8668 100644
--- a/man/boot.phylo.Rd
+++ b/man/boot.phylo.Rd
@@ -7,9 +7,10 @@
 \alias{plot.prop.part}
 \title{Tree Bipartition and Bootstrapping Phylogenies}
 \usage{
-boot.phylo(phy, x, FUN, B = 100, block = 1, trees = FALSE)
+boot.phylo(phy, x, FUN, B = 100, block = 1,
+           trees = FALSE, quiet = FALSE, rooted = FALSE)
 prop.part(..., check.labels = TRUE)
-prop.clades(phy, ..., part = NULL)
+prop.clades(phy, ..., part = NULL, rooted = FALSE)
 \method{print}{prop.part}(x, ...)
 \method{summary}{prop.part}(object, ...)
 \method{plot}{prop.part}(x, barcol = "blue", leftmar = 4, ...)
@@ -25,6 +26,9 @@ prop.clades(phy, ..., part = NULL)
     together (see details).}
   \item{trees}{a logical specifying whether to return the bootstraped
     trees (\code{FALSE} by default).}
+  \item{quiet}{a logical: a progress bar is displayed by default.}
+  \item{rooted}{a logical specifying whether the trees should be treated
+    as rooted or not (the default).}
   \item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
     series of such objects separated by commas, or (iii) a list
     containing such objects. In the case of \code{plot} further
@@ -44,7 +48,9 @@ prop.clades(phy, ..., part = NULL)
   These functions analyse bipartitions found in a series of trees.
 
   \code{prop.part} counts the number of bipartitions found in a series
-  of trees given as \code{\dots}.
+  of trees given as \code{\dots}. If a single tree is passed, the
+  returned object is a list of vectors with the tips descending from
+  each node (i.e., clade compositions indexed by node number).
 
   \code{prop.clades} counts the number of times the bipartitions present
   in \code{phy} are present in a series of trees given as \code{\dots} or
@@ -84,6 +90,10 @@ prop.clades(phy, ..., part = NULL)
   passed as \code{\dots} fulfills conditions (i) and (ii) above, then it
   might be faster to first call, e.g., \code{pp <- prop.part(...)}, then
   use the option \code{part}: \code{prop.clades(phy, part = pp)}.
+
+  You have to be careful that by default \code{prop.clades} considers
+  the trees as unrooted and this may result in spurious results if the
+  trees are rooted (see examples).
 }
 \value{
   \code{prop.part} returns an object of class \code{"prop.part"} which
@@ -117,10 +127,11 @@ prop.clades(phy, ..., part = NULL)
 }
 \examples{
 data(woodmouse)
-tr <- nj(dist.dna(woodmouse))
+f <- function(x) nj(dist.dna(x))
+tr <- f(woodmouse)
 ### Are bootstrap values stable?
 for (i in 1:5)
-  print(boot.phylo(tr, woodmouse, function(xx) nj(dist.dna(xx))))
+  print(boot.phylo(tr, woodmouse, f, quiet = TRUE))
 ### How many partitions in 100 random trees of 10 labels?...
 TR <- replicate(100, rtree(10), FALSE)
 pp10 <- prop.part(TR)
@@ -131,6 +142,13 @@ pp20 <- prop.part(TR)
 length(pp20)
 plot(pp10, pch = "x", col = 2)
 plot(pp20, pch = "x", col = 2)
+
+set.seed(1)
+tr <- rtree(10) # rooted by default
+prop.clades(tr, tr) # clearly wrong
+prop.clades(tr, tr, rooted = TRUE)
+tr <- rtree(10, rooted = FALSE)
+prop.clades(tr, tr) # correct
 }
 \keyword{manip}
 \keyword{htest}