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Nextclade

Table of contents

  • Home
  • Migration to Nextclade v3
  • Nextclade Web
    • Getting started
    • Analysis results table
    • Phylogenetic tree view
    • Export
    • Performance tips
    • URL parameters
    • Using local files with Nextclade Web
  • Nextclade CLI
    • Installation
      • Standalone download
      • With Docker
      • With Conda
      • Build from source
    • Usage
    • Reference
  • Nextclade datasets
  • Input files
    • Sequence data
    • Reference sequence
    • Genome annotation
    • Reference tree
    • Pathogen configuration
    • Compression, stdin
  • Output files
    • All outputs
    • Nucleotide alignment
    • Translations
    • Analysis results (tabular)
    • Analysis results (JSON)
    • Phylogenetic tree
    • Genome annotation of query sequences
    • Errors and warnings
    • Compression, stdout
  • Algorithm
    • 1. Sequence alignment
    • 2. Translation
    • 3. Phylogenetic placement
    • 4. Clade assignment
    • 5. Mutation calling
    • 6. Quality Control (QC)
    • 7. Detection of PCR primer changes
    • Nextclade as pango lineage classifier: Methods and Validation
  • Useful links
  • Frequently asked questions
  • Terminology
  • Developer documentation
    • Developer guide
    • macOS: development troubleshooting
  • Recent changes
    • 3.21.2
    • 3.21.1
    • 3.21.0
    • 3.20.0
    • 3.19.0
    • 3.18.1
    • 3.18.0
    • 3.17.0
    • 3.16.0
    • 3.15.3
    • 3.15.2
    • 3.15.1
    • 3.15.0
    • 3.14.5
    • 3.14.4
    • 3.14.3
    • 3.14.2
    • 3.14.1
    • 3.14.0
    • 3.13.3
    • 3.13.2
    • 3.13.1
    • 3.13.0
    • 3.12.0
    • 3.11.0
    • 3.10.2
    • 3.10.1
    • Nextclade 3.10.0
    • Nextclade 3.9.1
    • Nextclade 3.9.0
    • Nextclade 3.8.2
    • Nextclade 3.8.1
    • Nextclade 3.8.0
    • Nextclade 3.7.4
    • Nextclade 3.7.3
    • Nextclade 3.7.2
    • Nextclade 3.7.1
    • Nextclade 3.7.0
    • Nextclade 3.6.0
    • Nextclade 3.5.0
    • Nextclade 3.4.0
    • Nextclade 3.3.1
    • Nextclade 3.3.0
    • Nextclade 3.2.1
    • Nextclade 3.2.0
    • Nextclade 3.1.0
    • Nextclade 3.0.1
    • Nextclade 3.0.0
    • Older versions
Nextclade
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Recent changes

Table of contents

  • 3.21.2
  • 3.21.1
  • 3.21.0
  • 3.20.0
  • 3.19.0
  • 3.18.1
  • 3.18.0
  • 3.17.0
  • 3.16.0
  • 3.15.3
  • 3.15.2
  • 3.15.1
  • 3.15.0
  • 3.14.5
  • 3.14.4
  • 3.14.3
  • 3.14.2
  • 3.14.1
  • 3.14.0
  • 3.13.3
  • 3.13.2
  • 3.13.1
  • 3.13.0
  • 3.12.0
  • 3.11.0
  • 3.10.2
  • 3.10.1
  • Nextclade 3.10.0
  • Nextclade 3.9.1
  • Nextclade 3.9.0
  • Nextclade 3.8.2
  • Nextclade 3.8.1
  • Nextclade 3.8.0
  • Nextclade 3.7.4
  • Nextclade 3.7.3
  • Nextclade 3.7.2
  • Nextclade 3.7.1
  • Nextclade 3.7.0
  • Nextclade 3.6.0
  • Nextclade 3.5.0
  • Nextclade 3.4.0
  • Nextclade 3.3.1
  • Nextclade 3.3.0
  • Nextclade 3.2.1
  • Nextclade 3.2.0
  • Nextclade 3.1.0
  • Nextclade 3.0.1
  • Nextclade 3.0.0
  • Older versions
Previous Next

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

The core Nextstrain team is

Trevor Bedford , Richard Neher , Ivan Aksamentov , James Hadfield , Emma Hodcroft , John Huddleston , Jover Lee , Victor Lin , JT McCrone , 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.

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© Copyright 2020-2026, Trevor Bedford and Richard Neher

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