Nextstrain

Nextstrain takes the genome sequences that labs around the world share for a virus or bacterium and turns them into a family tree and a map, updated as new sequences come in.^1,2 Each tip of the tree is one sampled infection; branches that share mutations share an ancestor, so the tree shows which outbreaks are connected, roughly when a lineage jumped, and where it travelled.² Its front page lists continually updated views for H5N1 avian influenza, seasonal flu, measles, mpox, Ebola, tuberculosis, West Nile virus, SARS-CoV-2 and many more.¹

The picture is the full-genome view of the H5N1 outbreak in North American cattle, coloured by host: cattle in orange, birds in blue, other mammals in yellow and humans in red.⁵ When captured it showed 5,647 genomes sampled between November 2023 and August 2026, maintained by Louise Moncla and the Nextstrain team.⁵ The avian-flu build splits the cattle outbreak (genotype B3.13, from 2024) from the separate D1.1 jumps into cattle in 2025, and builds per-segment trees for H5N1, H5NX, H7N9 and H9N2.⁴

Augur is the pipeline that filters the sequences, aligns them and builds the trees.^2,6 Auspice draws them in the browser. Nextclade places a single sequence on a reference tree inside the browser, and Nextstrain Groups lets labs and health agencies publish their own analyses on the site.¹ The code is under the GNU Affero General Public License, and screenshots may be reused under CC BY 4.0 with credit to nextstrain.org.³ The site's copyright line names Trevor Bedford and Richard Neher; the core team page lists ten people.³

For someone modelling a place, Nextstrain is the measured side of an epidemic. Simulators such as OpenABM-Covid19 and MATSim EpiSim run what-ifs on a synthetic population. A tree like this one is what those what-ifs have to answer to. It can also be the first record that a shock from outside the model has arrived, as when a bird virus turned up in dairy herds.