True tree: (A,B) and (C,D) are the real sister pairs. A and C — one from each pair, non-sisters — have adjustable branch lengths. Watch what happens to parsimony as they lengthen.
True topology: ((A,B),(C,D)) | B and D have fixed short branches | A and C's branches are adjustable below
0.05
0.05
True tree
(A,B) | (C,D)
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Competing tree
(A,C) | (B,D)
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Lower score = fewer required character-state changes = preferred by maximum parsimony.