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PhylogeneticTrees :: pRing

pRing -- Constructs the ring of probability coordinates

Synopsis

Description

The probability coordinates for a phylogenetic tree model have one coordinate for each possible outcome of the model. A possible outcome is any labeling of the leaves of the tree by elements of the group G of the model. Thus the number of coordinates is |G|n where n is the number of leaves.

The variables use symbol p.

i1 : pRing(4,CFNmodel)

o1 = QQ[p       , p       , p       , p       , p       , p       , p       , p       , p       , p       , p       , p       , p       , p       , p       , p       ]
         0,0,0,0   0,0,0,1   0,0,1,0   0,0,1,1   0,1,0,0   0,1,0,1   0,1,1,0   0,1,1,1   1,0,0,0   1,0,0,1   1,0,1,0   1,0,1,1   1,1,0,0   1,1,0,1   1,1,1,0   1,1,1,1

o1 : PolynomialRing
i2 : pRing(3,JCmodel)

o2 = QQ[p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     , p     ]
         0,0,0   0,0,1   0,0,2   0,0,3   0,1,0   0,1,1   0,1,2   0,1,3   0,2,0   0,2,1   0,2,2   0,2,3   0,3,0   0,3,1   0,3,2   0,3,3   1,0,0   1,0,1   1,0,2   1,0,3   1,1,0   1,1,1   1,1,2   1,1,3   1,2,0   1,2,1   1,2,2   1,2,3   1,3,0   1,3,1   1,3,2   1,3,3   2,0,0   2,0,1   2,0,2   2,0,3   2,1,0   2,1,1   2,1,2   2,1,3   2,2,0   2,2,1   2,2,2   2,2,3   2,3,0   2,3,1   2,3,2   2,3,3   3,0,0   3,0,1   3,0,2   3,0,3   3,1,0   3,1,1   3,1,2   3,1,3   3,2,0   3,2,1   3,2,2   3,2,3   3,3,0   3,3,1   3,3,2   3,3,3

o2 : PolynomialRing

See also

Ways to use pRing :