I still don't quite understand. We have 
human:  C
chimp:  T
mouse:  T
rat:    C

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So which comparisons exactly lead to to a number of 2? With which rules?

As a poor perl programmer I'm not familiar with the phylogenetic tree, so if that's relevant here please explain in which relation these four examples appear in that tree.

In reply to Re^3: Maximal Parsimony Problem by moritz
in thread Maximal Parsimony Problem by neversaint

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