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arxiv: 1409.4130 · v2 · pith:DFRD7OKAnew · submitted 2014-09-15 · 🧮 math.AG · q-bio.PE

H-Representation of the Kimura-3 Polytope

classification 🧮 math.AG q-bio.PE
keywords mathbbrepresentationhalf-spacekimura-3modelpolytopetimestree
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Given a group-based Markov model on a tree, one can compute the vertex representation of a polytope which describes the associated toric variety. The half-space representation, however, is not easily computable. In the case of $\mathbb{Z}_2$ or $\mathbb{Z}_2\times\mathbb{Z}_2$, these polytopes have applications in the field of phylogenetics. We provide a half-space representation for the $m$-claw tree where $G=\mathbb{Z}_2\times\mathbb{Z}_2$, which corresponds to the Kimura-3 model of evolution.

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