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

Synopsis

• Usage:
phyloToricAMatrix(T,M)
phyloToricAmatrix(G,M)
phyloToricAMatrix(n,E,M)
• Inputs:
• T, an instance of the type LeafTree,
• 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,
• Outputs:
• , 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

Ways to use phyloToricAMatrix :

• "phyloToricAMatrix(Graph,Model)"
• "phyloToricAMatrix(LeafTree,Model)"
• "phyloToricAMatrix(ZZ,List,Model)"

For the programmer

The object phyloToricAMatrix is .