R: Phylogenetic Tree of 193 HIV-1 Sequences

hivtree {ape} | R Documentation

## 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

`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

[Package ape version 5.1 Index]