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PhylogeneticTrees : Index
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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