Augur
development version
(
71395958
)
Table of contents
Installation
Using Augur
Augur subcommands
augur parse
augur curate
normalize-strings
passthru
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
augur measurements
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 Public API
augur.io
Developer API
augur
augur.align
augur.ancestral
augur.clades
augur.dates
augur.dates.ambiguous_date
augur.dates.errors
augur.distance
augur.errors
augur.export
augur.export_v1
augur.export_v2
augur.filenames
augur.filter
augur.filter._run
augur.filter.include_exclude_rules
augur.filter.io
augur.filter.subsample
augur.filter.validate_arguments
augur.frequencies
augur.frequency_estimators
augur.import
augur.index
augur.io
augur.io.file
augur.io.json
augur.io.metadata
augur.io.print
augur.io.sequences
augur.io.shell_command_runner
augur.io.vcf
augur.lbi
augur.mask
augur.measurements
augur.measurements.concat
augur.measurements.export
augur.parse
augur.reconstruct_sequences
augur.refine
augur.sequence_traits
augur.titer_model
augur.titers
augur.traits
augur.translate
augur.tree
augur.types
augur.util_support
augur.util_support.color_parser
augur.util_support.color_parser_line
augur.util_support.node_data
augur.util_support.node_data_file
augur.util_support.node_data_reader
augur.utils
augur.validate
augur.validate_export
augur.version
Authors
Augur
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Augur
Developer API
augur
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augur.filenames
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Versions
latest
stable
22.0.2
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22.0.0
21.1.0
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21.0.0
20.0.0
19.3.0
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19.1.0
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18.2.0
18.1.2
18.1.1
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18.0.0
17.1.0
17.0.0
16.0.3
16.0.2
16.0.1
16.0.0
15.0.2
15.0.1
15.0.0
14.1.0
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13.1.2
13.1.1
13.1.0
13.0.4
13.0.3
13.0.2
13.0.1
13.0.0
12.1.1
12.1.0
12.0.0
11.3.0
11.2.0
11.1.2
11.1.1
11.1.0
11.0.0
10.3.0
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10.1.1
10.1.0
10.0.4
10.0.3
10.0.2
10.0.1
10.0.0
9.0.0
8.0.0
7.0.2
7.0.1
7.0.0
6.4.3
6.4.2
6.4.1
6.4.0
6.3.0
6.2.0
6.1.1
6.1.0
6.0.0
5.4.1
5.4.0
5.3.0
5.2.1
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5.1.1
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