Taxonium

The phylogenetic explorer that supports million-node trees

[Taxonium @Taxonium_]

https://t.co/asRJp9T3SQ

[Theo Sanderson @theosanderson]

🌲🧬Announcing the release of https://t.co/ATqYFdR5dC 2.0, and a new preprint!
The pandemic has seen an unprecented scale of sequencing. 11 million SARS-CoV-2 genomes are now available! Taxonium is the first tool to let you explore trees of this size. 🧵https://t.co/39CVDq4fHZ

[Emily Bruce, PhD @poisondartfrog7]

@TheMenacheryLab @hannah_kubinski 2/n As Delta was emerging, we saw that most of the viral sequencing surveillance showed that a cysteine had been introduced into the nucleocapsid protein, at residue 215 (great work from the Schuck group showed this was advantageous in the absence of other mutations in N or S)

[Taxonium @Taxonium_]

For example, the extraordinary PANGEA Consortium's HIV trees (https://t.co/1dIek3dWzo) – that w/ >15,000 genomes that can be CPU-intensive in Auspice – now can load from Charon in Taxonium:

POL - https://t.co/nDaPZ90HcR
GAG - https://t.co/e5ZN5S8ZPa
ENV - https://t.co/euNkfmrNHa

[Taxonium @Taxonium_]

Taxonium update: We have added a "proxy" feature to the Taxonium web app, which makes it easier to use URLs as input (it removes CORS restrictions).

This should make loading trees from URLs more reliable, and allows direct loading of public trees hosted with @Nextstrain Charon.

[Taxonium @Taxonium_]

Today we launch a new key feature.

🗝️🔑

[Chase W. Nelson 倪誠志 @chasewnelson]

Trying out TAXONIUM, a new tool for visualizing phylogenetic trees from @theosanderson at https://t.co/5tX0ONazXq

Testing it here to upload and visualize my own tree of 6264 HPVs.

Quick and smooth, easy to search, no glitches when zooming. I'll being using this from now on.
1/3

[Taxonium @Taxonium_]

https://t.co/3ofShIkrbg

[Theo Sanderson @theosanderson]

🎺 Delighted that the paper describing Taxonium is now out in @eLife. It describes the challenges that the influx of millions of SARS-CoV-2 genomes posed, and how https://t.co/ATqYFdRD3a allows you to explore the connections between them.
https://t.co/5qg93iCIXd

[antisense. @razoralign]

Taxonium, a web-based tool for exploring large phylogenetic trees https://t.co/uSUFN1PjxY

[Theo Sanderson @theosanderson]

And inevitably I found a bug after posting - if you downloaded please upgrade to the latest release or you might have issues loading bigger trees. https://t.co/aM56Ac0MIi Nicer auto-updating on the todo-list.

[Theo Sanderson @theosanderson]

I'm excited to announce the launch of the @Taxonium_ desktop app. For the smoothest way to explore large custom JSONL trees, give it a try.

Instructions at https://t.co/3xzINn4aQo

[antisense. @razoralign]

Treenome Browser: co-visualization of enormous phylogenies and millions of genomes https://t.co/9tHkppdS8r

[Taxonium @Taxonium_]

To improve this, we built a new taxoniumtools component, newick_to_taxonium, which allows you to build a Taxonium JSONL from a Newick tree.

Although Taxonium can load raw newick trees and metadata in the browser, pre-calculated JSONLs load faster. https://t.co/dTD0dZbvGe

[Theo Sanderson @theosanderson]

Spent an evening hacking together a new way of visually exploring the tree of life with NCBI Taxonomy, Wikipedia, and @Taxonium_
🌲🧬

https://t.co/dWKfwaaum9

[Taxonium @Taxonium_]

Whereas the "PANGO lineage" field on Cov2Tree used to be the lineage as calculated using PangoLearn, we are now instead using the monophyletic lineage annotated in the UShER tree. This reflects in part that an UShER-based method is now default in Pangolin. It looks nicer too!

[Taxonium @Taxonium_]

(or at least the 444, 460s)

[Taxonium @Taxonium_]

A Taxonium query to return these lineages: https://t.co/jUPWMa2PTQ

[Marc Johnson @SolidEvidence]

OK, I think I got them all. Convergent evolution on steroids.
@CorneliusRoemer @JosetteSchoenma @PeacockFlu @siamosolocani @LongDesertTrain

[NCBI @NCBI]

You can learn more about this project and other works completed at our Beyond Phylogenies codeathon here: https://t.co/b4iozaNxpx

👏 Thanks for sharing and for your hard work at the event! #OpenScience

[Taxonium @Taxonium_]

We've tweaked the Nextstrain JSON support so you can now open Nextstrain JSON files from hgPhyloplace (https://t.co/aQr603VV3Y) in Taxonium https://t.co/8XCICdne1e

[Russ Corbett @RussCorbett]

Are you ready to have your mind blown interactively exploring all genomic variation in 5M+ genomes?

Welcome to the treenome! https://t.co/az5lk2XK9s