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tskit-dev / what-is-an-arg-paper

Manuscript and code for the "What is an ARG?" paper
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Restructure "local trees" section #406

Closed jeromekelleher closed 10 months ago

jeromekelleher commented 10 months ago

A work in progress on the local trees section, trying to spell out why we think using a combinatorial encoding is useful and important.

Needs more work, but actually this seems quite an important insight...

hyanwong commented 10 months ago

Personally, I think the idea of locally unary nodes is the main thing that makes people think that the local trees don't encode the entire ARG. When someone says "local trees" they think of each tree as only consisting of nodes that are branch points. If we lose the locally unary nodes, I can see that there isn't enough information to reconstruct the ARG (i.e. including recombination nodes).

jeromekelleher commented 10 months ago

Merging an update to the local trees and the "unary" nodes section. It's a bit more formal now, but since there was lots of confusion, I think this can't be avoided.

Hopefully some basic questions about why we bother with formal definitions etc have been answered.