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