Jeremy G. Sumner

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I declare that this thesis contains no material which has been accepted for a degree or diploma by the University or any other institution, except by way of background information and duly acknowledged in the thesis, and that, to the best of my knowledge and belief, this thesis contains no material previously published or written by another person, except(More)
Though algebraic geometry over C is often used to describe the closure of the tensors of a given size and complex rank, this variety includes tensors of both smaller and larger rank. Here we focus on the n × n × n tensors of rank n over C, which has as a dense subset the orbit of a single tensor under a natural group action. We construct polynomial(More)
keywords: phylogenetics, model selection, General Time Reversible (GTR) model, closure The general time-reversible (GTR) model (Tavaré, 1986) has been the workhorse of molecular phylogenetics for the last decade. GTR sits at the top of the ModelTest hierarchy of models (Posada & Crandall, 1998) and, usually with the addition of invariant sites and a gamma(More)
We consider novel phylogenetic models with rate matrices that arise via the embedding of a progenitor model on a small number of character states, into a target model on a larger number of character states. Adapting representation-theoretic results from recent investigations of Markov invariants for the general rate matrix model, we give a prescription for(More)
We present an alternative method for calculating likelihoods in molecular phylogenetics. Our method is based on partial likelihood tensors, which are generalizations of partial likelihood vectors, as used in Felsenstein's approach. Exploiting a lexicographic sorting and partial likelihood tensors, it is possible to obtain significant computational savings.(More)
Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, there are usually extra constraints on the rates, depending on the situation. If a model is formulated in this way, it is possible(More)
We consider the continuous-time presentation of the strand symmetric phylogenetic substitution model (in which rate parameters are unchanged under nucleotide permutations given by Watson-Crick base conjugation). Algebraic analysis of the model's underlying structure as a matrix group leads to a change of basis where the rate generator matrix is given by a(More)
We present a general method of dimensional reduction for phylogenetic tree models. The method reduces the dimension of the model space from exponential in the number of extant taxa, to quadratic in the number of taxa. A key feature is the identification of an invariant subspace which depends only bilinearly on the model parameters; in contrast to the usual(More)
When the process underlying DNA substitutions varies across evolutionary history, some standard Markov models underlying phylogenetic methods are mathematically inconsistent. The most prominent example is the general time-reversible model (GTR) together with some, but not all, of its submodels. To rectify this deficiency, nonhomogeneous Lie Markov models(More)