Frederick A Matsen

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Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data are generated by a mixture model has stimulated considerable recent debate. Much of the controversy stems from simulations of mixture model data on a given tree topology for which(More)
In this paper, we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster model, which is a generalization of the two state symmetric (CFN) model. In particular, we show that the set of mixture(More)
Traditional language learning theory explores an idealized interaction between a teacher and a learner. The teacher provides sentences from a language, while the learner has to infer the underlying grammar. Here, we study a new approach by considering a population of individuals that learn from each other. There is no designated teacher. We are inspired by(More)
The "star paradox" in phylogenetics is the tendency for a particular resolved tree to be sometimes strongly supported even when the data is generated by an unresolved ("star") tree. There have been contrary claims as to whether this phenomenon persists when very long sequences are considered. This note settles one aspect of this debate by proving(More)
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