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).
- 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
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 ./addonmanager
The syntax to add new packages is:
addonmanager -add new_package