phyloToricAMatrix -- construct the design matrix of a group-based phylogenetic model

• Usage:

  phyloToricAMatrix(T,M)

  phyloToricAmatrix(G,M)

  phyloToricAMatrix(n,E,M)

• Inputs:
  • T, an instance of the type LeafTree,
  • G, a graph, a tree
  • n, an integer, the number of leaves
  • E, a list, the internal edges of the tree, given by the half the partition on leaves
  • M, an instance of the type Model,
• Outputs:
  • a matrix, whose columns parametrize the toric variety

i1 : phyloToricAMatrix(4, {{1, 2}},CFNmodel)

o1 = | 1 0 0 1 1 0 0 1 |
     | 0 1 1 0 0 1 1 0 |
     | 1 1 1 1 0 0 0 0 |
     | 0 0 0 0 1 1 1 1 |
     | 1 1 0 0 1 1 0 0 |
     | 0 0 1 1 0 0 1 1 |
     | 1 0 1 0 1 0 1 0 |
     | 0 1 0 1 0 1 0 1 |
     | 1 0 0 1 0 1 1 0 |
     | 0 1 1 0 1 0 0 1 |

              10       8
o1 : Matrix ZZ   <-- ZZ