+\name{speciesTree}
+\alias{speciesTree}
+\title{Species Tree Estimation}
+\description{
+ This function calculates the species tree from a set of gene trees.
+}
+\usage{
+speciesTree(x, FUN = min)
+}
+\arguments{
+ \item{x}{a list of trees, e.g., an object of class
+ \code{"multiPhylo"}.}
+ \item{FUN}{a function used to compute the divergence times of each
+ pair of tips.}
+}
+\details{
+ For all trees in \code{x}, the divergence time of each pair of tips is
+ calculated: these are then `summarized' with \code{FUN} to build a new
+ distance matrix used to calculate the species tree with a
+ single-linkage hierarchical clustering. The default for \code{FUN}
+ computes the maximum tree (maxtree) of Liu et al. (2010). Using
+ \code{FUN = sum} gives the shallowest divergence tree of Maddison and
+ Knowles (2006).
+}
+\value{
+ an object of class \code{"phylo"}.
+}
+\references{
+ Liu, L., Yu, L. and Pearl, D. K. (2010) Maximum tree: a consistent
+ estimator of the species tree. \emph{Journal of Mathematical Biology},
+ \bold{60}, 95--106.
+
+ Maddison, W. P. and Knowles, L. L. (2006) Inferring phylogeny despite
+ incomplete lineage sorting. \emph{Systematic Biology}, \bold{55}, 21--30.
+}
+\author{Emmanuel Paradis}
+\examples{
+### example in Liu et al. (2010):
+tr1 <- read.tree(text = "(((B:0.05,C:0.05):0.01,D:0.06):0.04,A:0.1);")
+tr2 <- read.tree(text = "(((A:0.07,C:0.07):0.02,D:0.09):0.03,B:0.12);")
+TR <- c(tr1, tr2)
+TSmax <- speciesTree(TR) # MAXTREE
+TSsha <- speciesTree(TR, sum) # shallowest divergence
+
+layout(matrix(1:4, 1))
+## playing with 'x.lim' is not so complicated
+## but this will be improved someday
+plot(tr1, "c", d = "u", y.lim = c(-0.07, 0.1), font = 1)
+axisPhylo(4); title("Gene tree 1")
+plot(tr2, "c", d = "u", y.lim = c(-0.05, 0.12), font = 1)
+axisPhylo(4); title("Gene tree 2")
+plot(TSmax, "c", d = "u", y.lim = c(-0.1, 0.07), font = 1)
+axisPhylo(4); title("Species tree inferred\nby MAXTREE")
+plot(TSsha, "c", d = "u", y.lim = c(0, 0.17), font = 1)
+axisPhylo(4); title("Species tree inferred\nby Shallowest Divergence")
+}
+\keyword{models}