- Tracer from http://tree.bio.ed.ac.uk/software/tracer/ helps you interpret the output of MrBayes in various useful and highly convenient ways. Everything that Tracer does can also be done using e.g. R, but Tracer is much quicker and easier for most purposes.
- It is also nice to have FigTree: http://tree.bio.ed.ac.uk/software/figtree/. Once again, FigTree doesn’t do anything that you can’t do in R, but it is very good for quick visualisations of trees.
- Make sure you have a text editor (not a word processor!), which allows you to edit plain ascii/unicode text. Atom is a good free one.
- RStudio provides the extremely useful R notebook format. This lets us combine text, code and output in reproducible documents. While teaching R is beyond the scope of my course, I will demonstrate some analyses using an R notebook, which will be published online (which should allow you to replicate these analyses in your own time).
- The basic workhorse for doing phylogenetics in R in the