Tree branch support

[matsen]

We have already seen lots of examples from @lauranoges where there is significant homoplasy, meaning that we have some apparent back-mutation.

I don't want to pull the trigger on these right yet, but some things to think about doing.

1. Apply a consensus tree method to the list of max parsimony trees
2. Calculate a consistency index or some such to measure this level of back-mutation
3. Use some network method? I think this is a bad idea but I had to include it.

We should probably do the first, but that's going to make Laura unhappy again because the branch lengths won't be interpretable in terms of level of mutation.

BTW, @lauranoges -- are all of these sequences observed once, or is there some (albeit noisy) measure of frequency?

[lauradoepker]

Which sequences, @matsen ? And is this referencing the conversation that Megan and I had with @psathyrella this morning?

[psathyrella]

sorry, I can't resist compensating for the emoji in the title not displaying:

[matsen]

I think the best is to show a single tree, along with either

1. A consensus tree of all of the MP trees
2. Branch support of that tree based on the other MP trees

[metasoarous]

We're putting this on Ice for now, and removing from the MB Release Milestone. It's still something we want to do, but we weren't able to make it in on this iteration, because of the issues that cropped up with prank (#131, #170) and the fact that we were banking on being able to use RaxML for computing support, but that we were depending on prank doing ancestral constructions separately for this. It's possible that we might get dnaml to do this, but I'd rather not wade through that arcana any more than I have to if there's any sliver of hope on the horizon for another method.

[matsen]

RAxML does give branch support cheaply, I believe.

In a sense, though, ecgtheow/linearham are there to integrate over the uncertainty we have in the trees, and the display that we have in Olmsted is to give a digestible overview. Thus, I'd suggest closing. @lauradoepker ?