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theosanderson / taxonium

A tool for exploring very large trees in the browser
http://taxonium.org
GNU General Public License v3.0
98 stars 17 forks source link

Feature: Add mpox tree to start page #249

Open corneliusroemer opened 2 years ago

corneliusroemer commented 2 years ago

Maybe add mpox to start page, similar to how Nextstrain displays the kind of trees one can see on the start page - would help discoverability etc.

ktmeaton commented 2 years ago

Would this be using the tree from the nextstrain monkeypox build? Or is there another pre-built public phylogeny?

theosanderson commented 2 years ago

There's a tree at https://mpx.taxonium.org/ . It's very much in beta atm, which is why it isn't on the front page. It uses data from LAPIS, as with NextStrain, and also takes inspiration from the NextStrain repo re: sequences to exclude and areas to mask, but is in some sense another phylogeny. The complete mess that generates it is at https://github.com/theosanderson/mpxtree, this will be made more solid in due course.

Atm it seems to disagree with NextStrain re the VA sequence. I'll have a look later at what's happening there soon.

ktmeaton commented 2 years ago

This is amazing thank you! I'll be cautious with usage and interpretation since it's in early development

theosanderson commented 2 years ago

The VA sequence is wrongly placed on mpxTree due to (in part, also lack of QC my side) https://github.com/cevo-public/mpox-spectrum-website/issues/10 - I'll remove it shortly

theosanderson commented 2 years ago

@all-contributors Please add @corneliusroemer for ideas

allcontributors[bot] commented 2 years ago

@theosanderson

I've put up a pull request to add @corneliusroemer! :tada: