Phylogenetics Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens

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ID: 329769
2026
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Abstract
MOTIVATION: Genome sequencing provides an exceptional window into the evolutionary and epidemiological dynamics of endemic and emerging pathogens, and thus allows for better, more targeted, public health interventions. Online genomic surveillance platforms can provide near real-time insight into these dynamics. RESULTS: Nextstrain provides continually updated real-time genomic surveillance for 21 viruses and the bacterial pathogen Mycobacterium tuberculosis, with most analyses relying solely on open sequence data. Each pathogen includes steps to fetch and curate open data, classify sequences using established nomenclature systems, perform phylogenetic analyses, and share the results publicly. These analyses are automated, with most running daily to provide continually updated snapshots of pathogen evolution. AVAILABILITY AND IMPLEMENTATION: All source code is available at https://github.com/nextstrain and a snapshot is archived at Zenodo (https://doi.org/10.5281/zenodo.22697730). Phylogenetic results can be visualized and downloaded at https://nextstrain.org/pathogens, and open sequence data and curated metadata are available at https://nextstrain.org/pathogens/files. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Authors Kimberly R. Andrews, Jennifer Chang, Cornelius Roemer, James Hadfield, Victor Lin, Anderson Fernandes Brito, Richard Olumide Daodu, I. A. Joia, Kathryn Kistler, Allison Li, Louise H. Moncla, Miguel I. Paredes, Denise Kühnert, Laura Marcela Torres, Laura Voitl, Ivan Aksamentov, Emma B. Hodcroft, John Huddleston, John T. McCrone, John S. J. Anderson, Thomas R. Sibley, Jover Lee, Richard A. Neher, Trevor Bedford
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag705
URL
https://doi.org/10.1093/bioinformatics/btag705
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