Augur
version 15.0.1
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
Creating a tree using your own tree builder
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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Augur
Using Augur
Augur subcommands
Edit on GitHub
augur version
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v: 15.0.1
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