Difference between revisions of "Phylogenetics: r8s Lab"
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First, create a directory for this lab in your home directory: | First, create a directory for this lab in your home directory: | ||
mkdir $HOME/r8slab | mkdir $HOME/r8slab | ||
| + | cd $HOME/r8slab | ||
Now, download the SAMPLE_SIMPLE data file there: | Now, download the SAMPLE_SIMPLE data file there: | ||
curl -o SAMPLE_SIMPLE http://hydrodictyon.eeb.uconn.edu/eeb349/SAMPLE_SIMPLE | curl -o SAMPLE_SIMPLE http://hydrodictyon.eeb.uconn.edu/eeb349/SAMPLE_SIMPLE | ||
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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: | 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: | ||
Revision as of 16:07, 19 April 2007
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This article is still under construction. Expect it to change frequently until this notice is removed. |
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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
