PhylogeneticTrees : Table of Contents
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PhylogeneticTrees -- A package to compute phylogenetic invariants associated to group-based models
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CFNmodel -- The model corresponging to the Cavender-Farris-Neyman model or binary Jukes Cantor
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edgeCut -- Breaks up a tree at an edge
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JCmodel -- The model corresponding to the Jukes Cantor model
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joinIdeal -- Computes the join of several ideals
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K2Pmodel -- The model corresponging to the Kimura 2-parameter model
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K3Pmodel -- The model corresponging to the Kimura 3-parameter model
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LeafTree -- A tree described in terms of its leaves
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Model -- A group-based model
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model -- Construct a Model
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phyloToric42 -- Compute the invariants of a group-based phylogenetic tree model using the 4ti2 package.
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phyloToricAMatrix -- Constructs the A matrix whose columns parametrize the toric variety of the tree T with n leaves
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phyloToricFP -- Compute the invariants of a group-based phylogenetic tree model using the toric fiber product structure
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phyloToricLinears -- Compute the linear invariants of a group-based phylogenetic tree model
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phyloToricQuads -- Compute the quadratic invariants of a group-based phylogenetic tree model
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phyloToricRandom -- Compute a random invariant of a group-based phylogenetic tree model using the toric fiber product structure
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pRing -- Constructs the ring of probability coordinates
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QRing -- Optional argument to specify Fourier coordinate ring
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qRing -- Constructs the ring of Fourier coordinates
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secant -- Computes the secant of an ideal
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