6 \title{Phylogenetic Tree of 193 HIV-1 Sequences}
9 This data set describes an estimated clock-like phylogeny of 193 HIV-1
10 group M sequences sampled in the Democratic Republic of Congo.
19 \code{hivtree.newick} is a string with the tree in Newick format.
20 The data frame \code{hivtree.table} contains the corresponding internode
25 This is a data example from Strimmer and Pybus (2001).
29 Strimmer, K. and Pybus, O. G. (2001) Exploring the demographic history
30 of DNA sequences using the generalized skyline plot. \emph{Molecular
31 Biology and Evolution}, \bold{18}, 2298--2305.
35 # example tree in NH format (a string)
36 data("hivtree.newick")
39 # generate file "hivtree.phy" in working directory
40 cat(hivtree.newick, file = "hivtree.phy", sep = "\n")
41 tree.hiv <- read.tree("hivtree.phy") # load tree
42 unlink("hivtree.phy") # delete the file "hivtree.phy"
46 # table with list of internode distances
51 # construct coalescence intervals
52 ci <- coalescent.intervals(tree.hiv) # from tree
53 ci <- coalescent.intervals(hivtree.table$size) #from intervals