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caporaso-lab / genome-sampler

https://caporasolab.us/genome-sampler/
BSD 3-Clause "New" or "Revised" License
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NEW: Root trees using an outgroup sample #63

Closed Oddant1 closed 3 years ago

Oddant1 commented 4 years ago

I think this is something along the lines of what we want here? Do we maybe want to use find_by_id instead of find? Additionally, some of the behavior of the root_at method seems a bit funky to me, but it may just be me misinterpreting the results.

image

The first tree in that image is unrooted. The second should be rooted at a. The third at f. The tree was already "rooted" at a, and telling it to actually root at a looks like it just replaced the a with the word root. So now we have no a. And I confirmed by trying to find a in that tree that a no longer exists.

a also inexplicably doesn't exist in the f rooted tree which also isn't actually rooted at f. Any time I tried to root at anything other than a I got something similar to the f rooted tree (i.e. something not actually rooted where I thought I told it to and without an a node)

ebolyen commented 3 years ago

Closing for now, we will try using iqtree2 for this functionality as node support is important and skbio cannot handle that at this time.