Software requirements

• MrBayes is a standalone package for Bayesian estimation of phylogenies. Install MrBayes from http://nbisweden.github.io/MrBayes/download.html; you also need to install the BEAGLE library to make this work on MacOSX
  • MacOSX: Click on the “mb” icon in the folder you’ve installed. You might get an error message about being forbidden to run programmes from “unidentified developers”: if so, got to “Security & Privacy” settings and click to button to allow this programme to run
  • If you know how, add this to your system path so you can start it by typing mb in the terminal
  • See also my crash course in commandline computing
• SplitsTree is a programme for visualising distance and tree sample data as a NeighborNet, an interesting technique for showing non-treelike histories. Install SplitsTree4 from http://www.splitstree.org/. By default the manual is included in the installation, but if you didn’t get it, the most recent version is available from http://ab.inf.uni-tuebingen.de/data/software/splitstree4/download/manual.pdf
• BayesTraits is a software package for phylogenetic comparative methods, such as MULTISTATE and DISCRETE. The current version is available from http://www.evolution.rdg.ac.uk/BayesTraitsV3.0.1/BayesTraitsV3.0.1.html; you should download the manual as well.

Optional tools

• 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 ape package