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petrelharp / num_edges

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Drop "Parsimony" paragraph? #16

Open jeromekelleher opened 4 days ago

jeromekelleher commented 4 days ago

I don't really see what it adds here, and it's trying to cover a lot of stuff at the moment. What's the point of opening this can of worms, this late in the paper?

petrelharp commented 4 days ago

Well, one reason I wanted to put it in was because I just went and read those papers, so wanted to give a historical nod to them. But a better reason is that I think what we're doing really does follow on from the previous "parsimony"-style papers (ie finding minimum number of recombinations); for instance, I wouldn't be surprised if the move we're describing here actually is discussed in, like, Simon's thesis or something. (I haven't checked carefully.) So, I think it's short, and would like to keep it?

But, maybe something like it would be better in the Introduction?

jeromekelleher commented 4 days ago

It's a good point. You could just mention this in the introduction in a sentence or two, with citations? A lot of the papers you're citing don't do parsimony at all (they're coalescent based things, really), and you're not citing a bunch of the parsimony ones.

The ARG paper tries to categorise this stuff fairly carefully in an appendix