Laboratory 2: Coalescent analysis, evolutionary genomics and selection
Handed out: November 8

Due: November 22

Tools: Lamarc program; PAML computer program; Molix knoppix cdrom

In this laboratory we will look at evolution both 'in the large' and 'in the small', by using the two biggest advances in evolutionary/population genetics over the past decade: (1) coalescent analysis; and (2) likelihood methods to detect selection. Most of all, we will want to stress the importance of looking at assumptions that an analysis method makes, and the effect it has on results.
See the interm tools documentation guide here.

To make your work a bit easier, we will be using a handy bootable CD-ROM of the Knoppix Linux system, that comes with pre-installed versions of the computer programs you will need. These systems are designed to work a PC. To use this modified Knoppix, you need to boot your PC from your CD-ROM drive. This is usually done by pressing a function key like F12 or F2 as you start up your PC, which will allow you to select your CD drive as a boot device. The screen will then present a 'boot:' line, and you need only hit carriage return. This will set up a running Linux system on your PC, without touching your hard drive. I'll demonstrate this in class. If your PC does not have a CD-ROM drive, or if you encounter other difficulties with this, please see us, and we can tell you how to download the programs individually.
Check with us if you need to run the program on Athena workstations rather than your own computer.
The remainder of the instructions for the laboratory are here.

Please remember to review the general instructions on the Laboratory Assignments page.