Teaching
Teaching
BGSMath course. Algebraic tools in phylogenetics. July 2022.
- 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".
- Resources:
- Small phylogenetic trees webpage. Notation explined in chapter 15 of Pachter-Sturmfels book above.