Phylogenetics: r8s Lab

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Expect it to change frequently until this notice is removed.
Adiantum.png EEB 349: Phylogenetics
The goals of this final lab are to learn how to: (1) set up a NEXUS file for the r8s program; (2) interpret the most important parts of the output of r8s; (4) view a tree with divergence times produced by r8s in TreeView.

Using r8s to estimate divergence times

There is no version of r8s for the Windows operating system, so we will use the version installed on the Bioinformatics cluster instead.

Start the program PuTTY and connect to bbcxsrv1.biotech.uconn.edu

If you do not find PuTTY on your desktop, you can download the program again from the PuTTY website. Using PuTTY, connect to bbcxsrv1.biotech.uconn.edu.

Download r8s

r8s is installed on the cluster, so we don't need the program itself, but we do need the sample data file that comes with r8s for the lab today. I've placed the SAMPLE_SIMPLE file that comes with r8s on a web server, and you can download it directly to the cluster using the curl program. Note that you could download the program using a web browser, then transfer the file to the cluster using PSFTP (or some other SFTP program), but using curl is easier and faster:

First, create a directory for this lab in your home directory: 

mkdir $HOME/r8slab
cd $HOME/r8slab

Now, download the SAMPLE_SIMPLE data file there: 

curl -o SAMPLE_SIMPLE http://hydrodictyon.eeb.uconn.edu/eeb349/SAMPLE_SIMPLE

Use the more command to see the first few lines of the SAMPLE_SIMPLE file. Note that r8s uses the NEXUS format for its input files. You can see more of the file by pressing the spacebar, and you can quit viewing the file by pressing the letter q (for quit).

See if you can answer these questions just by looking at the SAMPLE_SIMPLE file:

  • Which NEXUS blocks are present? (Hint: you should find 2 NEXUS blocks in this file)
  • Why does r8s need to know the number of sites? (as in the "blformat nsites =952 lengths=persite" command)

Below is the tree specified in the SAMPLE_SIMPLE file:

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