https://github.com/cran/ape
Tip revision: 1330e272d62c723b8073c95b066950b294f59697 authored by Emmanuel Paradis on 20 October 2012, 00:00:00 UTC
version 3.0-6
version 3.0-6
Tip revision: 1330e27
hivtree.Rd
\name{hivtree}
\alias{hivtree}
\alias{hivtree.newick}
\alias{hivtree.table}
\title{Phylogenetic Tree of 193 HIV-1 Sequences}
\description{
This data set describes an estimated clock-like phylogeny of 193 HIV-1
group M sequences sampled in the Democratic Republic of Congo.
}
\usage{
data(hivtree.newick)
data(hivtree.table)
}
\format{
\code{hivtree.newick} is a string with the tree in Newick format.
The data frame \code{hivtree.table} contains the corresponding internode
distances.
}
\source{
This is a data example from Strimmer and Pybus (2001).
}
\references{
Strimmer, K. and Pybus, O. G. (2001) Exploring the demographic history
of DNA sequences using the generalized skyline plot. \emph{Molecular
Biology and Evolution}, \bold{18}, 2298--2305.
}
\examples{
# example tree in NH format (a string)
data("hivtree.newick")
hivtree.newick
# generate file "hivtree.phy" in working directory
cat(hivtree.newick, file = "hivtree.phy", sep = "\n")
tree.hiv <- read.tree("hivtree.phy") # load tree
unlink("hivtree.phy") # delete the file "hivtree.phy"
plot(tree.hiv)
# table with list of internode distances
data("hivtree.table")
hivtree.table
# construct coalescence intervals
ci <- coalescent.intervals(tree.hiv) # from tree
ci <- coalescent.intervals(hivtree.table$size) #from intervals
ci
}
\keyword{datasets}