Taxonium

Taxonium is a tool for exploring trees.

How do I..

visualise my own Newick phylogeny?

Upload a Newick file to Taxonium.org, and optionally a metadata file in CSV or TSV format. If using a metadata file the leftmost column must contain names of the nodes as in the tree.

explore the global SARS-CoV-2 phylogeny?

Visit Cov2Tree.org which uses Taxonium to allow you to explore a tree built by researchers at UCSC using public data contributed by researchers across the world to the INSDC databases.

build my own mutation-annotated tree to explore in Taxonium, or add my own metadata to an existing phylogeny?

Use UShER to build a mutation-annotated tree. Then use taxoniumtools to convert it to a Taxonium format you can upload to the interface at Taxonium.org

You can also use taxoniumtools to add your own metadata to the existing public phylogeny.

Find out more in 📚 the documentation.

See Taxonium in action

Cov2Tree
Exploring the NCBI Taxonomy
Serratus (click Tree Viewer on any tree)
mpxTree

Citing Taxonium

Taxonium: a web-based tool for exploring large phylogenetic trees
Theo Sanderson
bioRxiv 2022.06.03.494608; doi: https://doi.org/10.1101/2022.06.03.494608

N.B. If you are citing the tree displayed at Cov2Tree.org, please cite the UCSC tree (.. and ideally Taxonium too if you relied on it for exploration)

Structure

Taxonium now consists of a number of components:

taxoniumtools - a Python package that lets you easily generate Taxonium files from Usher protobuf files
taxonium_web_client - the web client that is available at e.g. taxonium.org and let's you explore Taxonium files in your browser
taxonium_backend - a server-based backend that allows Taxonium trees to be explored without the user downloading the full tree (N.B. Taxonium can also be used without this backend, with static files acccessed in taxonium_web_client)
taxonium_data_handling - this is a node package upon which both the web client and the backend depend (it handles core logic common to both)