Taxonium, a web-based tool for exploring large phylogenetic trees

  1. Theo Sanderson  Is a corresponding author
  1. The Francis Crick Institute, United Kingdom
5 figures and 1 additional file


Tree exploration at unprecendented scale.

This figure presents a screenshot of the Taxonium web client displaying a 5,151,952 sequence tree of SARS-CoV-2 sequences. The left hand panel shows the zoomable tree with a minimap for orientation, and the right hand panel provides options for searching for nodes and for changing the colour scheme. Hovering over a node shows information in a tooltip, while clicking on a node displays further information in the right-hand panel. A search has been carried out for mutations at S:501 to Y, filtered to such nodes with at least 5,000 descendants, which are circled in red. Genomes are coloured by their PANGO lineage.

Components of the Taxonium project.

At the core of Taxonium is a graphical interface that runs in the web browser. It can connect either to a web-worker running in the same browser (for purely local use) or to an API web-server that serves parts of the tree on demand. Trees can be loaded from Newick format files with metadata TSVs (tab-separated value files), or from a specialised Taxonium JSONL (JSON-lines) format which is able to capture mutation-annotated trees. Taxonium JSONLs can be produced using the Taxoniumtools library.

Mutation-annotated trees capture full sequence variation.

In this screenshot, genotype data at position Spike 681 is overlaid onto the full SARS-CoV-2 tree with Taxonium. This analysis can be reproduced by setting the ‘Color by’ field to genotype.

Taxonium reveals recurrent mutations in SARS-CoV-2.

This figure shows a tree zoomed in on Omicron (B.1.1.529), with 1,422,024 sequences until late May 2022. Circled nodes feature a mutation at S:452 to either M or Q which have more than 10 descendants. These (independent) mutation are much more common on the BA.2 genetic background, revealing epistasis.

Taxonium has applications beyond SARS-CoV-2.

(A) Phylogeny of monkeypox sequences at The large clade represents the current outbreak (B) NCBI’s taxonomy of 2.2 M species as explorable at

Additional files

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Theo Sanderson
Taxonium, a web-based tool for exploring large phylogenetic trees
eLife 11:e82392.