3  Installation

3.1 Install required software:

• R Install latest version of R if possible

• Rstudio

• Figtree

• Geneious Free trial lasts for 30 days

• Beast 2 (Includes Beast, Beauti, TreeAnnotator)

• Tracer

3.2 Install required R packages

Open and run this script in Rstudio. This should install all required R packages (may take a while!).

install.packages('ape',dependencies = TRUE)
install.packages('phytools',dependencies = TRUE)
install.packages('paran')
install.packages('splits', repos='http://R-Forge.R-project.org')

If you have problems with installing package dependencies, this could be because you need to install a more recent version of R.

Check if packages load correctly:

library(ape)
library(phytools)
library(splits)