\name{bind.tree}
\alias{bind.tree}
\title{Binds Trees}
\usage{
bind.tree(x, y, where = "root", position = 0)
}
\arguments{
  \item{x}{an object of class \code{"phylo"}.}
  \item{y}{an object of class \code{"phylo"}.}
  \item{where}{an) integer giving the number of the node or tip of the
    tree \code{x} where the tree \code{y} is binded (\code{"root"} is a
    short-cut for the root).}
  \item{position}{a numeric value giving the position from the tip or
    node given by \code{node} where the tree \code{y} is binded;
    negative values are ignored.}
}
\description{
  This function binds together two phylogenetic trees to give a single
  object of class \code{"phylo"}.
}
\details{
  The argument \code{x} can be seen as the receptor tree, whereas
  \code{y} is the donor tree. The root of \code{y} is then sticked on a
  location of \code{x} specified by \code{where} and, possibly,
  \code{position}. If \code{y} has a root edge, this is added as in
  internal branch in the resulting tree.
}
\value{
  an object of class \code{"phylo"}.
}
\note{
  For the moment, this function handles only trees with branch lengths,
  and does not handle node labels.

  Further testing/improvements may be needed.
}
\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
\seealso{
  \code{\link{drop.tip}}, \code{\link{root}}
}
\examples{
### binds the two clades of bird orders
cat("((Struthioniformes:21.8,Tinamiformes:21.8):4.1,",
    "((Craciformes:21.6,Galliformes:21.6):1.3,Anseriformes:22.9):3.0):2.1;",
    file = "ex1.tre", sep = "\n")
cat("(Turniciformes:27.0,(Piciformes:26.3,((Galbuliformes:24.4,",
    "((Bucerotiformes:20.8,Upupiformes:20.8):2.6,",
    "(Trogoniformes:22.1,Coraciiformes:22.1):1.3):1.0):0.6,",
    "(Coliiformes:24.5,(Cuculiformes:23.7,(Psittaciformes:23.1,",
    "(((Apodiformes:21.3,Trochiliformes:21.3):0.6,",
    "(Musophagiformes:20.4,Strigiformes:20.4):1.5):0.6,",
    "((Columbiformes:20.8,(Gruiformes:20.1,Ciconiiformes:20.1):0.7):0.8,",
    "Passeriformes:21.6):0.9):0.6):0.6):0.8):0.5):1.3):0.7):1.0;",
    file = "ex2.tre", sep = "\n")
tree.bird1 <- read.tree("ex1.tre")
tree.bird2 <- read.tree("ex2.tre")
unlink(c("ex1.tre", "ex2.tre")) # clean-up
birds <- bind.tree(tree.bird1, tree.bird2, where = "root",
                   position = tree.bird1$root.edge)
birds
layout(matrix(c(1, 2, 3, 3), 2, 2))
plot(tree.bird1)
plot(tree.bird2)
plot(birds)
layout(matrix(1))
}
\keyword{manip}