Folks have asked what programs to install for class. For now, make sure you can get these working:
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Table of Contents
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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):
http://cran.r-project.org/bin/macosx/
For Windows:
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Where-can-I-find-the-latest-version_003f
Linux:
You presumably can figure this out yourself if you got Linux installed.
Mesquite
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.
http://mesquiteproject.org/mesquite/download/download.html
Tree viewers
Dendroscope: http://www-ab.informatik.uni-tuebingen.de/software/dendroscope
Figtree: http://tree.bio.ed.ac.uk/software/figtree/
Excel/OpenOffice
Excel will be handy, or if you don't have Office, get the free OpenOffice, which these days doesn't suck:
http://download.openoffice.org/
Text Editors
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.
Examples:
Windows - Notepad, Notetab
Mac - TextWrangler, BBedit
Advanced
For later in the course, download/install:
BEAST (and associated programs, including FigTree)
BayesTraits
Lagrange (which requires Enthought Python Distribution, a large download)