Toric varieties in phylogenetics
The paper contains a revised, and extended by new results, part of the author's PhD thesis. The main objects that we study are toric varieties naturally associated to special Markov processes on trees. Such Markov processes can be defined by a tree T and a group G. They are called group-based models. The main, but not unique, motivation to consider these processes comes from phylogenetics. We study the geometry, defining equations and combinatorial description of the associated toric varieties....