taxonium

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Dear @theosanderson, Could you help me build big trees of SC2, thanks.

liamxg

This is unreadable: Put a dark background below it

theosanderson

[pre-commit.ci] pre-commit autoupdate

1

updates: - [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.3.0...v4.6.0) - [github.com/pre-commit/mirrors-prettier: v2.7.1 → v4.0.0-alpha.8](https://github.com/pre-commit/mirrors-prettier/compare/v2.7.1...v4.0.0-alpha.8)

pre-commit-ci[bot]

Taxonium for bacteria

4

I know that some people have/are using Taxonium for bacterial genomes. I suspect that this probably poses some issues with e.g. the number of mutations on each branch which might...

theosanderson

Branch thickness / colour controlled by numerical property

7

Requested by @NicolaDM

theosanderson

Problem creating JOSNL file with newick_to_taxonium

8

Hi, I have a 3M tips tree that seems to large for the browser version of Taxonium, and I am trying to visualize it locally. I want to visualize mutations...

NicolaDM

Add WIP map view

9

This is a PR to add the WIP map view to Taxonium. Next steps: - Add scaled pie charts to map view ([ChatGPT](https://chat.openai.com/share/664b626d-8255-429b-8e0a-6390087affd0)) - Create a new backend route from...

simonbukin

Jbrowse fix and update

2

This updates jbrowse (for treenome browser) to 2.10.0, and also adds jbrowse peer dependencies I overlooked. The update (or peer deps) thankfully also seems to fix issues loading bam files.

amkram

https://taxonium.org/?treeUrl=https%3A%2F%2Fproxy.taxonium.org%2Fproxy%3Furl%3Dhttps%253A%252F%252Fnextstrain.org%252Fcharon%252FgetDataset%253Fprefix%253Dstaging%252Fnextclade%252Fsars-cov-2&ladderizeTree=true&treeType=nextstrain&xType=x_time does not work for whatever reason

theosanderson

Taxonium React Component Feedback

1

Hi, I was the student under @niemasd that was working to get the React component working on a web app (I've been a bit busy over the past month, apologies...

daniel-ji