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

View ORCID ProfileTheo Sanderson
doi: https://doi.org/10.1101/2022.06.03.494608
Theo Sanderson
1The Francis Crick Institute, UK
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  • For correspondence: theo.sanderson@crick.ac.uk
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Abstract

The COVID-19 pandemic has resulted in a step change in the scale of sequencing data, with more genomes of SARS-CoV-2 having been sequenced than any other organism on earth. Previous webbased tools for phylogenetic exploration were not able to directly scale to this size of tree. We have developed Taxonium, a new tool that uses WebGL to allow the exploration of trees with tens of millions of nodes. Taxonium allows visualisation of mutation-annotated trees, where the genotypes at each internal node are indicated, and also links each node to associated metadata. An optional server-side backend permits rapid loading for widely used datasets, while a client-only mode allows the exploration of niche or sensitive data. Taxonium is an open-source tool which can be applied to any large tree. We provide an application for exploring a public tree of more than five million SARS-CoV-2 sequences at cov2tree.org, the broader Taxonium tool at taxonium.org, and source code at github.com/theosanderson/taxonium.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://taxonium.org

  • http://cov2tree.org

  • http://docs.taxonium.org

  • https://github.com/theosanderson/taxonium

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 03, 2022.
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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
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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

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