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
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