hivtree

0th

Percentile

Phylogenetic Tree of 193 HIV-1 Sequences

This data set describes an estimated clock-like phylogeny of 193 HIV-1 group M sequences sampled in the Democratic Republic of Congo.

Keywords
datasets
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.

Aliases
  • hivtree
  • hivtree.newick
  • hivtree.table
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 = "")
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
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

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