Useful Software

Machine Learning

• libSVM - Support vector machine library for classification and/or regression.

Molecular Visualization

• VMD - 3D molecular visualization and animation. (Ubuntu: You'll need csh and libc++5 to have it running properly.)

Phylogenetic Networks

• SplitsTree - Computes phylogenetic trees and networks from molecular sequence data, distance matrices, etc.
• RaxML - ML Phylogenies

Statistical Analysis

• R - The R Project for Statistical Computing
  • Scott has put together a few R Notes