title: An algebraic analysis of the two state Markov model on tripod trees.
abstract: Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree, inferring conditions under which a given set of observations gives rise to such a model. This type of investigation has been undertaken before by several scientists from different fields of research. In contrast to other work we fully analyse the model, presenting conditions under which one can infer a model from the observation or at least get support for the tree-shaped interdependence of the leaves considered. We also present all conditions under which the results can be extended from tripod trees to quartet trees, a step necessary to reconstruct at least a topology. Apart from finding conditions under which such an extension works we discuss example cases for which such an extension does not work.
authors.affiliation: Department of Statistics and School of Biological Sciences, The University of Auckland, Auckland, New Zealand. steffen.klaere@gmail.com
authors.forename: Steffen
authors.initials: S
authors.lastname: Klaere
authors.forename: Volkmar
authors.initials: V
authors.lastname: Liebscher
mesh_terms: D008390:Markov Chains; D008957:Models, Genetic; D010802:Phylogeny