PhylogeneticTrees : Table of Contents
PhylogeneticTrees -- A package to compute phylogenetic invariants associated to group-based models
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
joinIdeal -- Computes the join of several ideals
K2Pmodel -- The model corresponging to the Kimura 2-parameter model
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
model -- Construct a Model
phyloToric42 -- Compute the invariants of a group-based phylogenetic tree model using the 4ti2 package.
phyloToricAMatrix -- Constructs the A matrix whose columns parametrize the toric variety of the tree T with n leaves
phyloToricFP -- Compute the invariants of a group-based phylogenetic tree model using the toric fiber product structure
phyloToricLinears -- Compute the linear invariants of a group-based phylogenetic tree model
phyloToricQuads -- Compute the quadratic invariants of a group-based phylogenetic tree model
phyloToricRandom -- Compute a random invariant of a group-based phylogenetic tree model using the toric fiber product structure
pRing -- Constructs the ring of probability coordinates
QRing -- Optional argument to specify Fourier coordinate ring
qRing -- Constructs the ring of Fourier coordinates
secant -- Computes the secant of an ideal
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