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transition vs. tranversion calc?

Diane Stothard dstothar at magnus.acs.ohio-state.edu
Tue Aug 16 10:15:46 EST 1994

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,

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