ArticleeLife2022
Taxonium, a web-based tool for exploring large phylogenetic trees.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens.Bioinformatics (Oxford, England) · 2026Article
- A generalized lineage nomenclature for viral genomic epidemiology.Nature microbiology · 2026Article
- Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data.Nature biotechnology · 2026Article
- ARGscape: a modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.Bioinformatics (Oxford, England) · 2026Article
- Climate-associated natural selection in the human mitochondrial genome.Molecular biology and evolution · 2026Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.Nature methods · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.Nature methods · 2026Article
- Compressive pangenomics using mutation-annotated networks.Nature genetics · 2026Article
- Datamonkey 3: browser-native molecular evolution analysis.Frontiers in bioinformatics · 2026Article
- SARS-CoV-2 within-host population expansion, diversification and adaptation in zoo tigers, lions and hyenas.Nature communications · 2025Article
- Article
- Highly Recurrent Multinucleotide Mutations in SARS-CoV-2.Molecular biology and evolution · 2025Article
- Circulation of SARS-CoV-2 and Co-Infection withInfectious disease reports · 2025Article
- UShER-TB: Scalable, Comprehensive, Accessible Phylogenomic Analysis ofmedRxiv : the preprint server for health sciences · 2025Article
- Evolution of the Nonvisual and Visual Opsin Gene Repertoire in Ray-Finned Fishes.Genome biology and evolution · 2025Article
- Genetic diversity of H9N2 avian influenza viruses in poultry across China and implications for zoonotic transmission.Nature microbiology · 2025Article
- Variant mutation G215C in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation.PLoS biology · 2025Article
- A Phylogenetic Method Identifies Candidate Drivers of the Evolution of the SARS-CoV-2 Mutation Spectrum.Molecular biology and evolution · 2025Article
- A phylogenetic method identifies candidate drivers of the evolution of the SARS-CoV-2 mutation spectrum.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
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. These sequences reveal key insights when represented as a phylogenetic tree, which captures the evolutionary history of the virus, and allows the identification of transmission events and the emergence of new variants. However, existing web-based tools for exploring phylogenies do not scale to the size of datasets now available for SARS-CoV-2. We have developed Taxonium, a new tool that uses WebGL to allow the exploration of trees with tens of millions of nodes in the browser for the first time. Taxonium links each node to associated metadata and supports mutation-annotated trees, which are able to capture all known genetic variation in a dataset. It can either be run entirely locally in the browser, from a server-based backend, or as a desktop application. We describe insights that analysing a tree of five million sequences can provide into SARS-CoV-2 evolution, and provide a tool at cov2tree.org for exploring a public tree of more than five million SARS-CoV-2 sequences. Taxonium can be applied to any tree, and is available at taxonium.org, with source code at github.com/theosanderson/taxonium.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.