PhylogeneticTrees : Index

• buckets -- the equivalence classes of group elements of a Model
• buckets(Model) -- the equivalence classes of group elements of a Model
• CFNmodel -- the model corresponding to the Cavender-Farris-Neyman model or binary Jukes Cantor
• digraph(LeafTree,List) -- convert a LeafTree to a Digraph
• digraph(LeafTree,Set) -- convert a LeafTree to a Digraph
• edgeContract -- contract an edge of a tree
• edgeContract(LeafTree,List) -- contract an edge of a tree
• edgeContract(LeafTree,Set) -- contract an edge of a tree
• edgeCut -- break up a tree at an edge
• edgeCut(LeafTree,List,Thing) -- break up a tree at an edge
• edgeCut(LeafTree,Set,Thing) -- break up a tree at an edge
• edges(LeafTree) -- list the edges of a tree
• fourierToProbability -- map from Fourier coordinates to probability coordinates
• fourierToProbability(Ring,Ring,ZZ,Model) -- map from Fourier coordinates to probability coordinates
• graph(LeafTree) -- convert a LeafTree to Graph
• group -- the group of a Model
• group(Model) -- the group of a Model
• internalEdges -- list the internal edges of a tree
• internalEdges(LeafTree) -- list the internal edges of a tree
• internalVertices -- list the internal vertices of a tree
• internalVertices(LeafTree) -- list the internal vertices of a tree
• isIsomorphic -- check isomorphism of two tree
• isIsomorphic(LeafTree,LeafTree) -- check isomorphism of two tree
• JCmodel -- the model corresponding to the Jukes Cantor model
• joinIdeal -- compute the join of several ideals
• joinIdeal(...,DegreeLimit=>...) -- compute the join of several ideals
• joinIdeal(Ideal,Ideal) -- compute the join of several ideals
• joinIdeal(List) -- compute the join of several ideals
• K2Pmodel -- the model corresponding to the Kimura 2-parameter model
• K3Pmodel -- the model corresponding to the Kimura 3-parameter model
• labeledBinaryTrees -- enumerate all binary labeled trees
• labeledBinaryTrees(ZZ) -- enumerate all binary labeled trees
• labeledTrees -- enumerate all labeled trees
• labeledTrees(ZZ) -- enumerate all labeled trees
• leafColorings -- list the consistent colorings of a tree
• leafColorings(LeafTree,Model) -- list the consistent colorings of a tree
• leafColorings(ZZ,Model) -- list the consistent colorings of a tree
• LeafTree -- a tree described in terms of its leaves
• leafTree -- construct a LeafTree
• LeafTree == LeafTree -- a tree described in terms of its leaves
• 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 model with 4ti2
• phyloToric42(...,QRing=>...) -- optional argument to specify Fourier coordinate ring
• phyloToric42(Graph,Model) -- compute the invariants of a group-based phylogenetic model with 4ti2
• phyloToric42(LeafTree,Model) -- compute the invariants of a group-based phylogenetic model with 4ti2
• phyloToric42(ZZ,List,Model) -- compute the invariants of a group-based phylogenetic model with 4ti2
• phyloToricAMatrix -- construct the design matrix of a group-based phylogenetic model
• phyloToricAMatrix(Graph,Model) -- construct the design matrix of a group-based phylogenetic model
• phyloToricAMatrix(LeafTree,Model) -- construct the design matrix of a group-based phylogenetic model
• phyloToricAMatrix(ZZ,List,Model) -- construct the design matrix of a group-based phylogenetic model
• phyloToricFP -- compute the invariants of a group-based phylogenetic model with toric fiber products
• phyloToricFP(...,QRing=>...) -- optional argument to specify Fourier coordinate ring
• phyloToricFP(LeafTree,Model) -- compute the invariants of a group-based phylogenetic model with toric fiber products
• phyloToricFP(ZZ,List,Model) -- compute the invariants of a group-based phylogenetic model with toric fiber products
• phyloToricLinears -- compute the linear invariants of a group-based phylogenetic model
• phyloToricLinears(...,QRing=>...) -- optional argument to specify Fourier coordinate ring
• phyloToricLinears(...,Random=>...) -- compute the linear invariants of a group-based phylogenetic model
• phyloToricLinears(LeafTree,Model) -- compute the linear invariants of a group-based phylogenetic model
• phyloToricLinears(ZZ,List,Model) -- compute the linear invariants of a group-based phylogenetic model
• phyloToricQuads -- compute the quadratic invariants of a group-based phylogenetic model
• phyloToricQuads(...,QRing=>...) -- optional argument to specify Fourier coordinate ring
• phyloToricQuads(...,Random=>...) -- compute the quadratic invariants of a group-based phylogenetic model
• phyloToricQuads(LeafTree,Model) -- compute the quadratic invariants of a group-based phylogenetic model
• phyloToricQuads(ZZ,List,Model) -- compute the quadratic invariants of a group-based phylogenetic model
• phyloToricRandom -- compute a random invariant of a group-based phylogenetic model
• phyloToricRandom(...,QRing=>...) -- optional argument to specify Fourier coordinate ring
• phyloToricRandom(LeafTree,Model) -- compute a random invariant of a group-based phylogenetic model
• phyloToricRandom(ZZ,List,Model) -- compute a random invariant of a group-based phylogenetic model
• pRing -- construct the ring of probability coordinates
• pRing(...,Variable=>...) -- construct the ring of probability coordinates
• pRing(LeafTree,Model) -- construct the ring of probability coordinates
• pRing(ZZ,Model) -- construct the ring of probability coordinates
• QRing -- optional argument to specify Fourier coordinate ring
• qRing -- construct the ring of Fourier coordinates
• qRing(...,Variable=>...) -- construct the ring of Fourier coordinates
• qRing(LeafTree,Model) -- construct the ring of Fourier coordinates
• qRing(ZZ,Model) -- construct the ring of Fourier coordinates
• rootedBinaryTrees -- enumerate all rooted binary trees
• rootedBinaryTrees(ZZ) -- enumerate all rooted binary trees
• rootedTrees -- enumerate all rooted trees
• rootedTrees(ZZ) -- enumerate all rooted trees
• secant -- compute the secant of an ideal
• secant(...,DegreeLimit=>...) -- compute the secant of an ideal
• secant(Ideal,ZZ) -- compute 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
• unlabeledTrees -- enumerate all unlabeled trees
• unlabeledTrees(ZZ) -- enumerate all unlabeled trees
• vertexCut -- break up a tree at a vertex
• vertexCut(LeafTree,List,Thing,Thing) -- break up a tree at a vertex
• vertexCut(LeafTree,Set,Thing,Thing) -- break up a tree at a vertex
• vertices(LeafTree) -- list the vertices of a tree