phyloToricAMatrix -- Constructs the A matrix whose columns parametrize the toric variety of the tree T with n leaves

Synopsis

• Usage:

  A = phyloToricAMatrix(T,M)

  A = phyloToricAmatrix(G,M)

  A = phyloToricAMatrix(n,E,M)

• Inputs:
  • T, an instance of the type LeafTree, A tree
  • G, an instance of the type 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, The model (CNFmodel, JCmodel, etc)
• Outputs:
  • A, a matrix, The matrix whose columns parametrize the toric variety

Description

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