PhylogeneticTrees : Index
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CFNmodel -- The model corresponging to the Cavender-Farris-Neyman model or binary Jukes Cantor
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edgeContract -- Contracts an edge of a tree
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edgeContract(LeafTree,List) -- Contracts an edge of a tree
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edgeContract(LeafTree,Set) -- Contracts an edge of a tree
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edgeCut -- Breaks up a tree at an edge
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edgeCut(LeafTree,List,Thing) -- Breaks up a tree at an edge
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edgeCut(LeafTree,Set,Thing) -- Breaks up a tree at an edge
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edges(LeafTree) -- List the edges of a tree
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fourierToProbability -- Map from Fourier coordinates to probablity coordinates
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fourierToProbability(Ring,Ring,ZZ,Model) -- Map from Fourier coordinates to probablity coordinates
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graph(LeafTree) -- Converts a LeafTree to Graph
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internalEdges -- Lists the internal edges of a tree
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internalEdges(LeafTree) -- Lists the internal edges of a tree
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internalVertices -- List the internal vertices of a tree
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internalVertices(LeafTree) -- List the internal vertices of a tree
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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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joinIdeal(...,DegreeLimit=>...) -- Computes the join of several ideals
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joinIdeal(Ideal,Ideal) -- Computes the join of several ideals
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joinIdeal(List) -- 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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leafColorings -- lists the friendly colorings of a tree
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leafColorings(LeafTree,Model) -- lists the friendly colorings of a tree
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leafColorings(ZZ,Model) -- lists the friendly colorings of a tree
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LeafTree -- A tree described in terms of its leaves
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leafTree -- Construct a LeafTree
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leafTree(Graph) -- Construct a LeafTree
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leafTree(List,List) -- Construct a LeafTree
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leafTree(ZZ,List) -- Construct a LeafTree
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leaves(LeafTree) -- List the leaves of a tree
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Model -- A group-based model
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model -- Construct a Model
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model(List,List,List) -- Construct a Model
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PhylogeneticTrees -- A package to compute phylogenetic invariants associated to group-based models
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phyloToric42 -- Compute the invariants of a group-based phylogenetic tree model using the 4ti2 package.
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phyloToric42(...,QRing=>...) -- Optional argument to specify Fourier coordinate ring
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phyloToric42(Graph,Model) -- Compute the invariants of a group-based phylogenetic tree model using the 4ti2 package.
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phyloToric42(LeafTree,Model) -- Compute the invariants of a group-based phylogenetic tree model using the 4ti2 package.
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phyloToric42(ZZ,List,Model) -- 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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phyloToricAMatrix(Graph,Model) -- Constructs the A matrix whose columns parametrize the toric variety of the tree T with n leaves
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phyloToricAMatrix(LeafTree,Model) -- Constructs the A matrix whose columns parametrize the toric variety of the tree T with n leaves
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phyloToricAMatrix(ZZ,List,Model) -- 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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phyloToricFP(...,QRing=>...) -- Optional argument to specify Fourier coordinate ring
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phyloToricFP(LeafTree,Model) -- Compute the invariants of a group-based phylogenetic tree model using the toric fiber product structure
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phyloToricFP(ZZ,List,Model) -- 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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phyloToricLinears(...,QRing=>...) -- Optional argument to specify Fourier coordinate ring
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phyloToricLinears(...,Random=>...) -- Compute the linear invariants of a group-based phylogenetic tree model
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phyloToricLinears(LeafTree,Model) -- Compute the linear invariants of a group-based phylogenetic tree model
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phyloToricLinears(ZZ,List,Model) -- 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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phyloToricQuads(...,QRing=>...) -- Optional argument to specify Fourier coordinate ring
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phyloToricQuads(...,Random=>...) -- Compute the quadratic invariants of a group-based phylogenetic tree model
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phyloToricQuads(LeafTree,Model) -- Compute the quadratic invariants of a group-based phylogenetic tree model
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phyloToricQuads(ZZ,List,Model) -- 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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phyloToricRandom(...,QRing=>...) -- Optional argument to specify Fourier coordinate ring
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phyloToricRandom(LeafTree,Model) -- Compute a random invariant of a group-based phylogenetic tree model using the toric fiber product structure
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phyloToricRandom(ZZ,List,Model) -- 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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pRing(LeafTree,Model) -- Constructs the ring of probability coordinates
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pRing(ZZ,Model) -- 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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qRing(LeafTree,Model) -- Constructs the ring of Fourier coordinates
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qRing(ZZ,Model) -- Constructs the ring of Fourier coordinates
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secant -- Computes the secant of an ideal
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secant(...,DegreeLimit=>...) -- Computes the secant of an ideal
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secant(Ideal,ZZ) -- Computes the secant of an ideal
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toricJoinDim -- Dimension of a join of toric varieties
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toricJoinDim(List) -- Dimension of a join of toric varieties
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toricJoinDim(Matrix,Matrix) -- Dimension of a join of toric varieties
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toricSecantDim -- dimension of a secant of a toric variety
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toricSecantDim(Matrix,ZZ) -- dimension of a secant of a toric variety
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vertexCut -- Breaks up a tree at a vertex
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vertexCut(LeafTree,List,Thing,Thing) -- Breaks up a tree at a vertex
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vertexCut(LeafTree,Set,Thing,Thing) -- Breaks up a tree at a vertex
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vertices(LeafTree) -- List the vertices of a tree