Ggtree

	EEB 5349: Phylogenetics

by Kevin Keegan

Goals

To introduce you to the R package ggtree for plotting phylogenetic trees.

Getting Started

Download the tree file (Paul can you host the treefile?)

Installing Packages

Open a terminal, start R, and install the packages we will be using. We'll be using the packages:

BiocInstaller
ape
Biostrings
ggplot2
ggtree
phytools
ggrepel
stringr
stringi
abind
treeio

You can install a package like so:

install.packages("BiocInstaller")

Read in the Tree File

We're dealing with a tree in the Newick file format:

tree <- read.newick("moth.txt")

There are ways to parse other tree file formats using other functions of the library/package treeio

Cite ggtree

citation("ggtree")

References

Yu G, Smith D, Zhu H, Guan Y and Lam TT (2017). “ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.” Methods in Ecology and Evolution, 8, pp. 28-36. doi: 10.1111/2041-210X.12628, http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract.