Résumé
Probabilistic models of character change/substitutions; Distance (minimum evolution, NJ, Fitch-Margoliash, etc.) and Parsimony methods; Likelihood and Bayesian methods; Tree search; Sources of error, both systematic and non-systematic, and approaches to address them: Stochastic variation, Model mis-specification (base composition; substitution matrices; others), Long-branch attraction, Taxon-sampling; others