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Introduction
What is Nextstrain?
Parts of a whole
Interpreting analyses
Pathogens
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Installing
Running a pathogen workflow
Creating a pathogen workflow
Exploring SARS-CoV-2 evolution
Creating a bacterial pathogen workflow
Writing a narrative
Analyzing genomes with Nextclade

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Bioinformatics
Sharing analyses
Communicating scientific insights
- Communicating Results Using Narratives
- Converting a narrative to PDF
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Reference

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Nextstrain

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Interpreting analyses

Learn how to interpret Nextstrain analyses.

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Revision e51a0018.

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

Nextstrain is built by

Trevor Bedford ,

Richard Neher ,

James Hadfield ,

Emma Hodcroft ,

Thomas Sibley ,

John Huddleston ,

Ivan Aksamentov ,

Kairsten Fay ,

Moira Zuber ,

Misja Ilcisin ,

Cassia Wagner ,

Louise Moncla ,

Allison Black ,

Miguel Parades ,

Barney Potter ,

Pavel Sagulenko ,

Charlton Callender

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 2022, Trevor Bedford and Richard Neher

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