Just came across this while looking for some info on character trait evolution:
2011 Bodega workshop – Phylogenetics wiki
It includes some great lecture slides and tutorials from a workshop on applied phylogenetics held in March 2011. The tutorials cover software packages like MrBayes, RAxML, R, BEAST, BayesTraits and topics including model selection, divergence dating, discrete & continuous character evolution, diversification rates.
There is also some good advice for aspiring phylogeneticists, including advice on becoming a programmer.
BacPathGenomics 