PhylogeneticTrees : Table of Contents

• PhylogeneticTrees -- a package to compute phylogenetic invariants associated to group-based models
• buckets -- 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
• edgeContract -- contract an edge of a tree
• edgeCut -- break up a tree at an edge
• edges(LeafTree) -- list the edges of a tree
• fourierToProbability -- map from Fourier coordinates to probability coordinates
• graph(LeafTree) -- convert a LeafTree to Graph
• group -- the group of a Model
• internalEdges -- list the internal edges of a tree
• internalVertices -- list the internal vertices of a tree
• isIsomorphic -- check isomorphism of two tree
• JCmodel -- the model corresponding to the Jukes Cantor model
• joinIdeal -- 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
• labeledTrees -- enumerate all labeled trees
• leafColorings -- list the consistent 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 model with 4ti2
• phyloToricAMatrix -- construct the design matrix of a group-based phylogenetic model
• phyloToricFP -- compute the invariants of a group-based phylogenetic model with toric fiber products
• phyloToricLinears -- compute the linear invariants of a group-based phylogenetic model
• phyloToricQuads -- compute the quadratic invariants of a group-based phylogenetic model
• phyloToricRandom -- compute a random invariant of a group-based phylogenetic model
• pRing -- construct the ring of probability coordinates
• QRing -- optional argument to specify Fourier coordinate ring
• qRing -- construct the ring of Fourier coordinates
• rootedBinaryTrees -- enumerate all rooted binary trees
• rootedTrees -- enumerate all rooted trees
• secant -- compute the secant of an ideal
• toricJoinDim -- dimension of a join of toric varieties
• toricSecantDim -- dimension of a secant of a toric variety
• unlabeledTrees -- enumerate all unlabeled trees
• vertexCut -- break up a tree at a vertex
• vertices(LeafTree) -- list the vertices of a tree