About

Introduction
What is Nextstrain?
Parts of a whole
Augur → Auspice
Interpreting analyses
Pathogens
Nextstrain Groups

Tutorials

Installing
Running a phylogenetic workflow
Creating a phylogenetic workflow
Exploring SARS-CoV-2 evolution
Creating a bacterial phylogenetic workflow
Writing a narrative
Analyzing genomes with Nextclade
Using a pathogen repository
- Running an ingest workflow
Creating a pathogen repository
- Creating an ingest workflow

How-to Guides

Bioinformatics
Sharing analyses
Communicating scientific insights
- Communicating Results Using Narratives
- Converting a narrative to PDF
Viewing previous analyses
Managing an installation
Contributing

Components

Augur
Auspice
Nextstrain CLI
Nextclade CLI
nextstrain.org

Reference

Glossary
Data formats
Data files
FAQ
CA certificate trust stores
Snakemake style guide
Documentation style guide
Governance

Nextstrain

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Communicating scientific insights

How-to guides for communicating understanding through Nextstrain-developed approaches

Table of contents

Communicating Results Using Narratives
Converting a narrative to PDF

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Hadfield et al., Nextstrain: real-time tracking of pathogen evolution , Bioinformatics (2018)

The core Nextstrain team is

Trevor Bedford ,

Richard Neher ,

Ivan Aksamentov ,

John SJ Anderson ,

Jennifer Chang ,

James Hadfield ,

Emma Hodcroft ,

John Huddleston ,

Cornelius Roemer ,

Please see the team page for more details.

All source code for Nextstrain is freely available under the terms of an open-source license, typically AGPL-3.0 or MIT. Refer to specific projects for details. Screenshots may be used under a CC-BY-4.0 license and attribution to nextstrain.org must be provided.

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, Josh Batson, David Blazes, Jesse Bloom, Peter Bogner, Anderson Brito, Matt Cotten, Ana Crisan, Tulio de Oliveira, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Nate Grubaugh, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Duncan MacCannell, Erick Matsen, Sebastian Maurer-Stroh, Placide Mbala, Danny Park, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Cecile Viboud for comments, suggestions and data sharing.

© Copyright 2025, Trevor Bedford and Richard Neher

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