Along the lines of this discussion, does anyone know how to calculate a MATRIX
of substitutions, i.e., the proportions of A->G, A->C, A->T, C->A, etc., for
all possible substitutions? I believe it is essential for doing analyses such
as weighted parsimony. I too have tried doing this using MacClade but again,
the problem is that it generates the matrix based upon a given tree. I would
like to know if there is a program that will generate this matrix with a given
outgroup and in-taxa only.
Thanks in advance,