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PhylogeneticTrees :: phyloToric42

phyloToric42 -- compute the invariants of a group-based phylogenetic model with 4ti2

Synopsis

Description

This function computes the invariants of a group-based phylogenetic tree model by computing the transpose of the matrix that encodes the defining monomial map and then using the function toricMarkov of the FourTiTwo package.

i1 : T = leafTree(4, {{0,1}})

o1 = {{0, 1, 2, 3}, {set {0, 1}, set {0}, set {1}, set {2}, set {3}}}

o1 : LeafTree
i2 : phyloToric42(T, CFNmodel)

o2 = ideal (- q       q        + q       q       , - q       q        +
               0,1,1,0 1,0,0,1    0,1,0,1 1,0,1,0     0,0,1,1 1,1,0,0  
     ------------------------------------------------------------------------
     q       q       )
      0,0,0,0 1,1,1,1

o2 : Ideal of QQ[q       , q       , q       , q       , q       , q       , q       , q       ]
                  0,0,0,0   0,0,1,1   0,1,0,1   0,1,1,0   1,0,0,1   1,0,1,0   1,1,0,0   1,1,1,1

See also

Ways to use phyloToric42 :

For the programmer

The object phyloToric42 is a method function with options.