Structured coalescent analyses with BEAST 2

Activity by Tim Vaughan, 26 January 2018


Running this activity

This activity can be completed either with your own installation of BEAST 2 or with the installation on the Amazon Machine Image. The first option is recommended if you have Java JDK 8 (NOT Java JDK 9) and BEAST v.2.4.7 or above installed, or if you have the time to install both before starting the activity. Alternatively, you can run the activity by connecting to the Amazon Machine Image through X2Go.


If you use your own installation of BEAST 2

  • Follow the instructions on www.beast2.org/ceskykrumlov2018/ for tutorial “Full structured coalescent inference using MultiTypeTree”, under “2. Structured Coalescent tutorials”.
  • Follow the instructions on www.beast2.org/ceskykrumlov2018/ for tutorial “Approximate structured coalescent inference using MASCOT”, under “2. Structured Coalescent tutorials”.


If you use the BEAST 2 installation on the Amazon Machine Image

  • Use X2Go to connect to the Amazon Machine Image.
  • Follow the instructions on www.beast2.org/ceskykrumlov2018/ for the tutorials “Full structured coalescent inference using MultiTypeTree” and then “Approximate structured coalescent inference using MASCOT”, both under “2. Structured Coalescent tutorials”. While doing so, please note the following:

    The MultiTypeTree and MASCOT packages are already part of the BEAST 2 installation on the AMI, so you can skip section “Installing the MultiTypeTree package” of the MultiTypeTree tutorial and section “Download MASCOT” of the MASCOT tutorial.

    You will find links to the required programs of the BEAST 2 package, including BEAST2, BEAUti, TreeAnnotator, Tracer, and FigTree on the Desktop of the Amazon Machine Image. You can start these programs by double-clicking, or by using right-click and “Open”. When you open BEAST, BEAUti, or TreeAnnotator, you will be asked if you want to “run BEAST2/BEAUti/TreeAnnotator or display its contents?”. It is important that you then select “Run in Terminal” in each case. You should not be asked the same question when opening Tracer.

    Input data will be loaded through BEAUti as described in the tutorials.

    If you start BEAST 2 with the link placed on the Desktop, then the output files will be written to the Desktop. If you start it by clicking on the BEAST 2 executable in “~/software/beast/bin/”, the output files will be written there.

  • If you should not be able to finish the BEAST 2 analysis, you can find pre-generated result files for the MultiTypeTree tutorial in directory “~/workshop_materials/07_beast2_structured_coalescent/multitypetree/pre_generated_logs” (these are identical to those linked in the tutorial) and for the MASCOT tutorial in directory “~/workshop_materials/07_beast2_structured_coalescent/mascot/pre_generated_logs”.