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

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 serverbased 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.

Automated Agnostic Designation of Pathogen Lineages

“…Statistics such as lineage size, associated mutations, and geographic localization are computed and reported as a part of a pull request to the curated Pango repository. Our update includes links to external data exploration sources such as cov-spectrum (Chen et al 2022) and taxonium (Sanderson 2022; Kramer et al 2022), as well as programmatic generation of all files requisite for the incorporation of the new designations. All code for this procedure can be found at https://github.com/jmcbroome/autolin.…”

Tracking and curating putative SARS-CoV-2 recombinants with RIVET

“…The table can be searched and sorted using any field, and the recombinant ancestors can be queried using sample identifiers. The table also links each recombinant to a Taxonium/Treenome view (Sanderson, 2022; Kramer et al ., 2023), in which the phylogenetic contexts and genotype information of the recombinant and its parent sequences can be simultaneously visualized (Figure 1B). The frontend also provides a view of single-nucleotide variation (SNV) in the three sequences (each recombinant and its parents), with informative sites highlighted (Figure 1C).…”

Treenome Browser: co-visualization of enormous phylogenies and millions of genomes

“…Treenome Browser further increases performance by subsampling nodes and mutations. Because many nodes occupy essentially the same spatial position when the tree is zoomed out, Taxonium dynamically displays sparsified trees from the full tree ( Sanderson, 2022 ). Treenome Browser also uses these subsampled trees when displaying mutations to avoid unneeded computation.…”

“…This site is preloaded with annotations for the reference genome (RefSeq NC_045512v2) curated by the UCSC Genome Browser ( Lee et al , 2022 ). We also support user-provided mutation-annotated trees created with UShER, which can be produced using the TaxoniumTools package ( Sanderson 2022 ) and loaded at taxonium.org .…”

“…The ongoing coronavirus disease 2019 pandemic has particularly stressed existing bioinformatic infrastructure for the analysis of genomic data. We developed UShER ( Turakhia et al , 2021 ) to enable the inference of a continuously growing phylogeny containing millions of SARS-CoV-2 genomes ( McBroome et al , 2021 ) and Taxonium to enable interactive exploration of phylogenies of this size ( Sanderson, 2022 ). Gingr ( Treangen et al , 2014 ) and the UCSC Genome Browser can display a multiple sequence alignment alongside a phylogeny ( Lee et al , 2022 ).…”