Geodesic
Brownian motion tree models are toric
Kybernetika, Tome 56 (2020) no. 6, pp. 1154-1175
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Felsenstein's classical model for Gaussian distributions on a phylogenetic tree is shown to be a toric variety in the space of concentration matrices. We present an exact semialgebraic characterization of this model, and we demonstrate how the toric structure leads to exact methods for maximum likelihood estimation. Our results also give new insights into the geometry of ultrametric matrices.
Felsenstein's classical model for Gaussian distributions on a phylogenetic tree is shown to be a toric variety in the space of concentration matrices. We present an exact semialgebraic characterization of this model, and we demonstrate how the toric structure leads to exact methods for maximum likelihood estimation. Our results also give new insights into the geometry of ultrametric matrices.
DOI : 10.14736/kyb-2020-6-1154
Classification : 15B48, 62H22, 62R01
Keywords: Brownian motion tree model; ultrametric matrices; toric geometry 
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Sturmfels, Bernd; Uhler, Caroline; Zwiernik, Piotr. Brownian motion tree models are toric. Kybernetika, Tome 56 (2020) no. 6, pp. 1154-1175. doi: 10.14736/kyb-2020-6-1154

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