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Augur version: 11.2.0
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Table of contents

  • Installation
  • Using Augur
    • Augur subcommands
      • augur parse
      • augur index
      • augur filter
      • augur mask
      • augur align
      • augur tree
      • augur refine
      • augur ancestral
      • augur translate
      • augur reconstruct-sequences
      • augur clades
      • augur traits
      • augur sequence-traits
      • augur lbi
      • augur distance
      • augur titers
      • augur frequencies
      • augur export
      • augur validate
      • augur version
      • augur import
    • Format of augur output
    • Environment variables
  • Augur Releases & Upgrading
    • Changelog
    • Augur v6 Release Notes
    • Migrating from augur v5 to v6
    • Breaking Changes to augur
    • Compatibility between Augur & Auspice versions
  • Frequently Asked Questions
    • The concept of a ‘build’
    • Preparing Your Metadata
    • Labeling clades
    • Specifying `refine` rates
  • Examples of Augur in the wild
  • Python Development API
    • augur package
      • augur.util_support package
        • augur.util_support.color_parser module
        • augur.util_support.color_parser_line module
        • augur.util_support.date_disambiguator module
        • augur.util_support.metadata_file module
        • augur.util_support.node_data module
        • augur.util_support.node_data_file module
        • augur.util_support.node_data_reader module
        • augur.util_support.shell_command_runner module
      • augur.align module
      • augur.ancestral module
      • augur.clades module
      • augur.distance module
      • augur.export module
      • augur.export_v1 module
      • augur.export_v2 module
      • augur.filenames module
      • augur.filter module
      • augur.frequencies module
      • augur.frequency_estimators module
      • augur.import module
      • augur.import_beast module
      • augur.index module
      • augur.lbi module
      • augur.mask module
      • augur.parse module
      • augur.reconstruct_sequences module
      • augur.refine module
      • augur.sequence_traits module
      • augur.titer_model module
      • augur.titers module
      • augur.traits module
      • augur.translate module
      • augur.tree module
      • augur.utils module
      • augur.validate module
      • augur.validate_export module
      • augur.version module
  • Authors
Augur
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  • Python Development API »
  • augur package »
  • augur.util_support package
  • Edit on GitHub

augur.util_support package¶

Submodules¶

  • augur.util_support.color_parser module
  • augur.util_support.color_parser_line module
  • augur.util_support.date_disambiguator module
  • augur.util_support.metadata_file module
  • augur.util_support.node_data module
  • augur.util_support.node_data_file module
  • augur.util_support.node_data_reader module
  • augur.util_support.shell_command_runner module
Next Previous

Revision 8df4b4d3.

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 , Jover Lee , Kairsten Fay , Sidney Bell , Colin Megill , Barney Potter , Pavel Sagulenko , Charlton Callender , Misja Ilcisin , Louise Moncla , Allison Black , Anderson Brito , Nate Grubaugh
All source code is freely available under the terms of the GNU Affero General Public License. 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, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Nathan Yozwiak for comments, suggestions and data sharing.
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© Copyright 2014–2021 Trevor Bedford and Richard Neher
Revision 8df4b4d3.

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