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
hivtree.newick is a string with the tree in Newick format.
The data frame 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. Molecular
Biology and Evolution, 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