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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