Re: Maximal Parsimony Problem

[psini]

I think that the idea is that given the tree:

$tree = '(mouse,rat,(human,chimp))'

the values in column 11 should be treated like this: (T,C,(C,T)) and so the value of 2 results from T ne C ne (C,T); whereas for instance column 3 leads to (G,A,(A,A)) and G ne A eq (A,A).

This is just a wild guess but, if I understand the logic right, (T,C,(A,G))=>3 and (T,C,(C,A))=>2. If it is so, the algorithm should not be so simple when more complex trees are involved.