Folks have asked what programs to install for class. For now, make sure you can get these working:
R Statistical Computing Language
R comes in lots of flavors, I recommend something that has a GUI (graphical user interface) rather than being completely pure command line.
I also recommend installing a precompiled package rather than trying to compile raw source code.
For Macs (10.5 or later, packages for older systems are available):
You presumably can figure this out yourself if you got Linux installed.
Mesquite is useful for manipulating character data, but fairly clumsy (not hopeless) with trees. Sometimes, when you just want to look at a tree, these can be easier.
Excel will be handy, or if you don't have Office, get the free OpenOffice, which these days doesn't suck:
Download a text editor, or find out where you have a text editor on your computer. A "pure text" editor does just ASCII text, no formatting, which is useful for saving your R commands, cutting/pasting them into the R GUI, etc.
Windows - Notepad, Notetab
Mac - TextWrangler, BBedit
For later in the course, download/install:
BEAST (and associated programs, including FigTree)
Lagrange (which requires Enthought Python Distribution, a large download)