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
• edgeContract -- Contracts an edge of a tree
• edgeCut -- Breaks up a tree at an edge
• edges(LeafTree) -- List the edges of a tree
• fourierToProbability -- Map from Fourier coordinates to probablity coordinates
• graph(LeafTree) -- Converts a LeafTree to Graph
• internalEdges -- Lists the internal edges of a tree
• internalVertices -- List the internal vertices of a tree
• 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
• leafColorings -- lists the friendly colorings of a tree
• LeafTree -- A tree described in terms of its leaves
• leafTree -- Construct a LeafTree
• leaves(LeafTree) -- List the leaves of a tree
• 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
• toricJoinDim -- Dimension of a join of toric varieties
• toricSecantDim -- dimension of a secant of a toric variety
• vertexCut -- Breaks up a tree at a vertex
• vertices(LeafTree) -- List the vertices of a tree