*eye roll*
Honestly, we try to beat that stuff out of them in calculus and you people just reinforce it all over again.
Maximum parsimony is very similar to the traveling salesman problem.
Interesting. Is there a fractional relaxation?
On a highly conserved protein, verifying it isn't difficult.
Again, this is the icky proof-by-example, I talked about. One of the reasons we hate this sort of thing is that it makes you reinvent the wheel everytime. Just show it works for all proteins. Or, better yet, for all strings on a fixed alphabet.
Indeed. It's transparent. A beautiful demonstration of molecular evolution, suitable for a freshman class.
Actually, it's a demonstration of a model which purports to...
What stuff? Don't you get it? We're interested in generating trees. We care if the trees are unique. We care that the trees are correct. That is pretty much all we care about. In general, for the task of generating a tree for a 100 amino acid, highly conserved protein, over 20 organisms, you can generate a maximally parsimonious tree by brute force; heck, I can usually do it by inspection. But having a program certainly helps.
If I were doing bioinformatics research, I'd care about the scalability and computability of my algorithms. I'm not. I'm trying to show freshman students who often don't know what DNA is when the class starts, how the DNA of various species can be used to generate a tree of life.
Interesting. Is there a fractional relaxation?
I don't know, and care less.
Again, this is the icky proof-by-example, I talked about. One of the reasons we hate this sort of thing is that it makes you reinvent the wheel everytime. Just show it works for all proteins. Or, better yet, for all strings on a fixed alphabet.
Who's we? You and the small subset of other pure mathematicians with a chip on their shoulder about the real world?
As far as I'm concerned, mathematics is a tool for the sciences. We're happy to have mathematicians work out the gory details of algorithmic computability, on the admittedly over optimistic hope they might come up with something useful.