[AmishDude]

"ribosomal protein" and "s7" are particular terms and "widely separated" and "maximum parsimony tree" are, in an of themselves are also particular terms with particular meanings that cannot be immediately deciphered from the individual words. If you think they can, note that the term "maximum parsimony tree" is, in fact, defined as a minimum of some function. To the uninitiated, it isn't clear what function you are optimizing, let alone that it is a minimum.

The scaling of the problem is irrelevant if you're talking about small numbers of organisms

That's what makes it monkey-work. It's just an algorithm. Grab the handle. Turn the crank. There's your answer. The real questions are: Can you prove that the algorithm always gives a maximum parsimony tree? That's "proof" now. Not proof-by-example. What is the average-time performance? What conditions on the sequences will fail to produce average-time performance? Can they be considered "unnatural"? Can you construct a tree in polynomial time such that the number of changes to connect all elements on the tree is always at most (1+epsilon)M where M is the minimum and epsilon is a fixed positive constant.

Now if you present a proof in class that the algorithm always terminates and always produces the MPT, then that would be a good start.

[Right Wing Professor]

That's what makes it monkey-work. It's just an algorithm. Grab the handle. Turn the crank. There's your answer. The real questions are: Can you prove that the algorithm always gives a maximum parsimony tree? That's "proof" now. Not proof-by-example. What is the average-time performance? What conditions on the sequences will fail to produce average-time performance? Can they be considered "unnatural"? Can you construct a tree in polynomial time such that the number of changes to connect all elements on the tree is always at most (1+epsilon)M where M is the minimum and epsilon is a fixed positive constant.

These are exercises for a math class, not a biology class.

Get a clue.