Table of contents
- Extended Bayesian Skyline Plots (EBSP) with BEAST2
- Structured coalescent analyses with BEAST2 (using the packages MultiTypeTree and BASTA)
- Bayes Factor Delimitation of Species (*with genomic data; BFD*) with BEAST2
A website for all BEAST2 exercises of the Workshop is provided at http://beast2.org/ceskykrumlov2016/. If you haven’t yet installed BEAST2 on your machine, please do so now, as described on http://beast2.org/ceskykrumlov2016/.
If for some reason the installation fails on your machine, you may run these exercises on an AMI, however, the latest version of BEAST2, v.2.3.3 pre3 is only available on a dedicated AMI called “WPSG 2016 BEAST”. So if the BEAST2 installation was not possible on your own machine, then please start a new instance of this dedicated AMI just like you did previously with the general Workshop AMI, described here, and connect to this AMI using X2Go. (if you have questions, please let us know). To start BEAUti on this AMI, double-click the program icon and choose “Run” (not “Run in Terminal”) in the appearing dialog window. However in order to run BEAST2, use a Terminal window of the AMI, navigate to where you saved the xml file after using BEAUti, and type “beast” to execute the program.
If you have BEAST2 installed on your own machine, please download the full EBSP exercise material using the link below, and follow the instructions included in the download.
If you’re using the AMI, you will find the input files for this exercise in directory ~/wpsg_2016/activities/beast/ebsp2-tut/mystery-mammal/, and the R script used for plotting in ~/wpsg_2016/activities/beast/ebsp2-tut/scripts/.
Please note that one of the functions (plotEBSPTimesHist; on page 13 of the tutorial) may produce an error with the R script included in the exercise material. You could skip this function, or if you want to run it, please download an updated version of the script from here.
If you don’t have time to wait for your own analyses to finish, you may find the provided log files of a fully converged EBSP analysis useful. These can be downloaded with the link below, or can be found on the AMI in directory ~/wpsg_2016/activities/beast/ebsp2-tut/mystery-long/.
- full EBSP exercise material
- EBSP exercise instructions only
- Log files for a fully converged run of the EBSP exercise
Just like for all other BEAST2 activities, we recommend running these exercises locally on your own machine, but they can also be run in very much the same way on the dedicated BEAST AMI. If using this AMI, note that the tree viewer IcyTree, which is used as part of the exercise is bookmarked in Firefox on the AMI.
The structured coalescent activity includes two exercises, one using full structured coalescent inference with the BEAST2 add-on MultiTypeTree, and one using approximate structured coalescent inference with the add-on BASTA.
The MultiTypeTree exercise will use a template dataset that can be loaded through BEAUti (as described in the instructions). The second exercise will build on the first, by manually editing the xml file prepared in the first exercise to run with BASTA.
- MultiTypeTree exercise instructions
- Log files for a fully converged run of the MultiTypeTree exercise
- BASTA exercise instructions
- Log files for a fully converged run of the BASTA exercise
Again, please run this exercise locally on your own machine unless you had difficulties installing BEAST2. If you run this on your own machine, please download the full BFD* exercise material using the link below.
If you run this exercise on the AMI, you’ll only have to download the BFD* exercise instructions with the link below. On the dedicated BEAST AMI, input data for the exercise can be found in ~/wpsg_2016/activities/beast/BFDstar-tutorial/.