Species delimitation with SNAPP

Activity by Huw Ogilvie, 30 January 2018

Running this activity

This activity can be completed either with your own installation of BEAST 2 (SNAPP is an add-on package to BEAST 2) or with the BEAST 2 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.

Note that in order to keep the activity time reasonably short, you should not run analyses for all models as described in step 13 (section 6.5) of the tutorial. Instead, choose one of the alternative models (RunB to RunG) in addition to the RunA model. By sharing results with other Workshop participants in the end of the activity we can then compare all models with each other.

If you use your own installation of BEAST 2

  • Follow the instructions on www.beast2.org/ceskykrumlov2018/ for tutorial “3. Species delimitation with SNAPP”. 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, TreeAnnotator, Tracer). You can start these programs by double-clicking, or by using right-click and “Open”. When you open BEAST 2, 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.

    The SNAPP and Model_Selection packages are already part of the BEAST 2 installation on the AMI, so you can skip section “6.1 Downloading the programs” and steps 3 and 4 of section “6.2 Setting up the XML file with BEAUTi” in the tutorial pdf. Thus, start the tutorial with step 5 in section 6.2.

    The input file in Nexus format (“smallhemi129.nex”) required in step 6 of section 6.2 is located in “~/workshop_materials/10_snapp/data/”. Instead of “Import Alignment” (as specified in the pdf), the menu option for loading input is actually called “Add Alignment”.

    When you write the file named “RunA.xml” at the end of step 10 in section 6.2, please save it in directory “~/workshop_materials/10_snapp/runs/RunA”.

    When you specify the “rootdir” in step 11 of section 6.3, use the full path to the “RunA” directory: “/home/wpsg/workshop_materials/10_snapp/runs/RunA” (without the quotes). Also make sure to change the chain length from the default to 1000 (this is not mentioned in the tuturial but is required to keep run times around 10 minutes.

    Write down the marginal L estimate reported at the end of the path sampling analysis in step 12 of section 6.4, as shown in Figure 13 of the tutorial. You will need to compare this estimate to estimates for alternative species delimitation models. Don’t close the PathSampler window until after step 15 (section 6.6).

    Because the manual editing of xml files described in step 13 (section 6.5) of the tutorial may be a bit too tedious through X2Go, the xml files “RunB.xml” to “RunG.xml” are already prepared in directories “~/workshop_materials/10_snapp/runs/RunB” to “~/workshop_materials/10_snapp/runs/RunG”. Nevertheless, please read section 6.5 to find out which changes were made and why.