Taxonium, a web-based tool for exploring large phylogenetic trees
- The Francis Crick Institute, United Kingdom
Figures
Figure 1
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.
Figure 2
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.
Figure 3
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.
Figure 4
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.
Figure 5
Taxonium has applications beyond SARS-CoV-2.
(A) Phylogeny of monkeypox sequences at mpx.taxonium.org. The large clade represents the current outbreak (B) NCBI’s taxonomy of 2.2 M species as explorable at taxonomy.taxonium.org.
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Taxonium, a web-based tool for exploring large phylogenetic trees
eLife 11:e82392.
https://doi.org/10.7554/eLife.82392
