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

Krämer, Alexander; Sanderson, Theo; Corbett‐Detig, Russ

doi:10.1093/bioinformatics/btac772

Cited by 6 publications

(5 citation statements)

References 5 publications

(8 reference statements)

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“…In addition, statistics such as lineage size, associated mutations and geographic localization can be computed and reported to the user. Our update includes links to external data exploration sources such as CoV-Spectrum 10 and Taxonium 11 , 12 , as well as the 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 .…”

Section: Resultsmentioning

confidence: 99%

A framework for automated scalable designation of viral pathogen lineages from genomic data

McBroome,

de Bernardi Schneider,

Roemer

et al. 2024

Nat Microbiol

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Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.

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Section: Resultsmentioning

confidence: 99%

A framework for automated scalable designation of viral pathogen lineages from genomic data

McBroome,

de Bernardi Schneider,

Roemer

et al. 2024

Nat Microbiol

Self Cite

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“…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).…”

Section: Resultsmentioning

confidence: 99%

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

Smith

Cheng

Turakhia

2023

Preprint

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Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that are being shared online every day is quite challenging, causing many recombinants to be missed or suffer from weeks of delay in being formally identified while undergoing expert curation. We present RIVET - a software pipeline and visual platform that takes advantage of recent algorithmic advances in recombination inference to comprehensively and sensitively search for potential SARS-CoV-2 recombinants, and organizes the relevant information in a web interface that would help greatly accelerate the process identifying and tracking recombinants.

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“…1C and Supplementary Methods ), which can display a subtree of descendant recombinant sequences in the Auspice interactive phylogeny viewer ( Hadfield et al 2018 ). For the public tree, the table also provides a link to a Taxonium/Treenome view ( Sanderson 2022 , Kramer et al 2023 ) for each recombinant, in which the phylogenetic contexts and genotype information of the recombinant and its parent sequences can be simultaneously visualized ( Fig. 1C and Supplementary Methods ).…”

Section: Resultsmentioning

confidence: 99%

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

Smith,

Ye,

Turakhia

2023

Bioinformatics

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Motivation Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that are being shared online every day is quite challenging, causing many recombinants to be missed or suffer from weeks of delay in being formally identified while undergoing expert curation. Results We present RIVET—a software pipeline and visual platform that takes advantage of recent algorithmic advances in recombination inference to comprehensively and sensitively search for potential SARS-CoV-2 recombinants and organize the relevant information in a web interface that would help greatly accelerate the process of identifying and tracking recombinants. Availability RIVET-based web interface displaying the most updated analysis of potential SARS-CoV-2 recombinants is available at https://rivet.ucsd.edu/. RIVET’s frontend and backend code is freely available under the MIT license at https://github.com/TurakhiaLab/rivet and the documentation for RIVET is available at https://turakhialab.github.io/rivet/. The inputs necessary for running RIVET’s backend workflow for SARS-CoV-2 are available through a public database maintained and updated daily by UCSC (https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/). Supplementary information Supplementary data are available at Bioinformatics online.

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

Cited by 6 publications

References 5 publications

A framework for automated scalable designation of viral pathogen lineages from genomic data

A framework for automated scalable designation of viral pathogen lineages from genomic data

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

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

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