Running and Verifying BEAST 2

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the nexus directory.

   cd /path/to/BEAST/beast/examples/nexus

3. Run the following command. The BEAUti 2: Standard window is displayed, as shown in Figure 1.

   beauti

   Figure 1 BEAUti 2: Standard
   
4. Import a sequence.
   Choose File > Import Alignment. The Open dialog box is displayed. Select the Primates.nex sequence file in the nexus directory, as shown in Figure 2.

   Figure 2 Primates.nex sequence file
   
5. Link or unlink partition models (Click Open and the following dialog box is displayed).

   Generally, aligned gene sequence information is imported during analysis. However, in some cases, partitions may also exist. If joint analysis is required, link partition models. Otherwise, unlink them.

   

6. Set the substitution model.

   For the nucleotide substitution model, you can select GTR, HKY, JC69, or TN93. Gamma Category Count can be set to a value ranging from 4 to 8. HKY and 4 are selected here as an example. Other parameters such as Substitution Rate, Shape (the shape parameter of gamma distribution), and Frequencies are estimated in the analysis.

   

7. Set the molecular clock.

   Click the Clock Model tab. Parameters include Strict Clock, Relaxed Clock Exponential, and Relaxed Clock Log Normal. If Strict Clock is selected, the rate difference between molecules in the model is not considered.

   

8. Set verification information.
   1. Click Priors and set Tree.t:firsthalf and Tree.t:secondhalf to Yule Model. Retain the default settings for other parameters.

      

   2. Click +Add Prior at the bottom of the Priors area. In the window that is displayed, select Tree.t:secondhalf. In Taxon set editor, define a name, for example, fossil information. Select two species (for example, Homo_sapiens and Pan) whose divergence time needs to be calibrated and move them to the right border.

      

      Select Normal in the monophyletic drop-down list to verify the distribution information. Set the divergence time. The divergence of Homo sapiens and Pan is between 5 and 7 My. Therefore, set the center point of the normal distribution to 6 My and the standard deviation to 0.5 My, and select monophyletic.

      

      

9. Click MCMC to set the MCMC options.

   

   Chain Length: 10,000,000 (by default)

   tracelog: The chain is sampled once every 1000 times.

   screenlog: The log is displayed on the screen every 1000 times.

   treelog.t:tree: The topology is printed every 1000 times.

10. Save the XML file.

    Choose File > Save As and define an output file name to generate an XML file.

    

11. Perform a BEAST test.

    beast -threads 128 test01.xml

    Check the value of Total calculation time (in seconds) in the Primates.log file. A smaller value indicates higher performance.

    The following is an example of the output result: