Commonly used phylogenetic methods, Monash HPC access and basic bioinformatics

This folder contains a bunch of notes from the BEAST 2017 workshop, held in London, 24 - 29 July. Unfortunately, these only contain the notes for lectures in which I actually understood stuff.


  • BEAST is incredibly mathematical.
  • The primary output of BEAST (and BEAST2) is a probability distribution of trees. I guess that this is a discrete distribution of n trees, where each tree has a probability P(Treei), for i = 1...n. Different model, prior or initial parameter specifications will ultimately affect P(Treei).

Workshop Resources

  • Program
  • Slides. Unfortunately, these are of limited utility without the speaker present to tell you what's happening. Still, they're not completely useless.

Moving from BEAST to BEAST2

Install these add-ons in BEAUTi: - bdsky - BDSKY functionality - MASCOT - StarBeast2 - CLASSIC_BEAST - presumably BEAST1 functionality - SNAPP - BDSSM - SCOTTI - BACTER

These are a bunch of add-ons that were introduced in the workshop, some not very relevant, but get them anyway. To install a package, go to File --> Manage Packages. Select the package that you wish to install, and click the Install\Upgrade button. Restart BEAUTi for the changes to take effect.

Command Line Option: use addon manager to do this. To see a list of what you can do with it:

cd path/to/BEAST 2.4.7

The syntax to add new packages is: addonmanager -add new_package