Species network inference with BEAST 2

Activity by Huw Ogilvie, 31 January 2018

Note that this activity will be given as an optional exercise during the Open Lab in the evening of 31 January.

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.

The BEAST 2 analysis itself is going to take about 30 minutes (time for a long coffee break or for joining the Open Lab).

If you use your own installation of BEAST 2

  • Follow the instructions on www.beast2.org/ceskykrumlov2018/ for tutorial “4. Species network inference 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 input file in Nexus format, named “3s_6loci.nex”, is located in “~/workshop_materials/14_species_network/data”.

    The SpeciesNetwork package is already part of the BEAST 2 installation on the AMI, so you can skip section “Installing SpeciesNetwork” in the tutorial pdf. Thus, start the tutorial with section “Switching the template”.

    If you find that manually writing the new file “3s_6loci_sum.xml” for section “Viewing the species networks” (page 14) of the tutorial is too tedious through X2Go, you can find this file already prepared in directory “~/workshop_materials/14_species_network/example_xmls”. Before running it with BEAST 2, make sure that it is located in the same directory as the file “speciesnetwork.trees” resulting from the first BEAST 2 analysis. The easiest way to do so might be to copy it from “~/workshop_materials/14_species_network/example_xmls” to the Desktop by right-clicking the file and selecting “Copy to > Desktop”.