Teaching

Slides: introduction (L1), evolutionary models (L2), results on simulations and real data (L5)
Main references:

E.Allman J.Rhodes The mathematics of phylogenetics, lecture notes. For Markov processes on phylogenetic trees
L. Pachter, B. Sturmfels (editors), Algebraic statistics for computational biology Cambridge University Press 2005. For the algebraic part (phylogenetic algebraic geometry).
N. Eriksson, K. Ranestad, B. Sturmfels, S. Sullivant, Phylogenetic algebraic geometry. in "Projective varieties with unexpected properties " de Gruyter 2005.
J. Fernández-Sánchez, M. Casanellas, Invariant Versus Classical Quartet Inference When Evolution is Heterogeneous Across Sites and Lineages, Systematic biology 2016. Erik+2 method reported on the slides "results on simulations and real data".

Small phylogenetic trees webpage. Notation explained in chapter 15 of Pachter-Sturmfels book above.