Demography inference with BEAST 2

Activity by Tim Vaughan, 22 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 for tutorial “1. Extended Bayesian Skyline Plot (EBSP) tutorial”. You will find a pdf with activity instructions within the zip directory for this tutorial.

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

  • Download the tutorial instructions in pdf format from here.
  • Use X2Go to connect to the Amazon Machine Image.
  • While following the tutorial described in the pdf, keep in mind the following:

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

    The directory with input data, named “mystery-mammal”, is located in “~/workshop_materials/04_beast2_demography”.

    The output files of BEAST 2 (files with extensions .log and .trees) will not be written as described in the pdf to directory “~/workshop_materials/04_beast2_demography/mystery-run”, but instead on the Desktop if you start BEAST 2 with the link placed on the Desktop, or in “~/software/beast/bin/” if you start BEAST 2 by clicking on the executable in that location. You should move these output files into directory “~/workshop_materials/04_beast2_demography/mystery-run” if you want to follow the rest of the exercise as literally as possible.

    The R script required in section 2.2 of the tutorial is located in “~/workshop_materials/04_beast2_demography/scripts”. To run it, use RStudio through your local browser (Firefix, Chrome, Safari should all work), not through X2Go, and type the IP address of your AMI instance followed by “:8787” in the URL bar. This should open RStudio. Then type setwd("~/workshop_materials/04_beast2_demography/mystery-run") in RStudio, and then follow the guidelines in section 2.2 of the tutorial pdf.

  • If you should not be able to finish the BEAST 2 analysis in section 2, you can find pre-generated log files in directory “~/workshop_materials/04_beast2_demography/logs_for_a_100M_run”, which you can use in section 2.1.