Parsimony
Maximum Likelihood
RAxML Tutorial
GARLI (version 0.951 graphical) Tutorial
GARLI (version 0.96) Tutorial
Note on GARLI: The most recent version of GARLI is GARLI 1.0 (released Dec 2009), which is the finalized version of the beta release, GARLI 0.96b. The 0.96 tutorial is still applicable to GARLI 1.0.
Bayesian Inference
MrBayes Tutorial
Bruce Rannala's lecture on reconstructing trees with Bayesian methods.
