Augur
stable version
(26.0.0)
Table of contents
Installation
Using Augur
Augur subcommands
augur parse
augur curate
passthru
normalize-strings
format-dates
titlecase
apply-geolocation-rules
apply-record-annotations
abbreviate-authors
parse-genbank-location
transform-strain-name
rename
augur merge
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
augur read-file
augur write-file
Format of augur output
Environment variables
Augur Releases & Upgrading
Changelog
Deprecated features
Augur v6 Release Notes
Migrating from augur v5 to v6
Compatibility between Augur & Auspice versions
Frequently Asked Questions
What is a “build”?
How do I prepare metadata?
How do I label
clades
?
How do I specify
refine
rates?
How do I use my own tree builder?
Examples of Augur in the wild
Python Public API
augur.io
Developer API
augur package
augur.curate package
augur.curate.abbreviate_authors module
augur.curate.apply_geolocation_rules module
augur.curate.apply_record_annotations module
augur.curate.format_dates module
augur.curate.format_dates_directives module
augur.curate.normalize_strings module
augur.curate.parse_genbank_location module
augur.curate.passthru module
augur.curate.rename module
augur.curate.titlecase module
augur.curate.transform_strain_name module
augur.data package
augur.dates package
augur.dates.ambiguous_date module
augur.dates.errors module
augur.filter package
augur.filter.constants module
augur.filter.include_exclude_rules module
augur.filter.io module
augur.filter.subsample module
augur.filter.validate_arguments module
augur.filter.weights_file module
augur.import_ package
augur.import_.beast module
augur.io package
augur.io.file module
augur.io.json module
augur.io.metadata module
augur.io.print module
augur.io.sequences module
augur.io.shell_command_runner module
augur.io.strains module
augur.io.vcf module
augur.measurements package
augur.measurements.concat module
augur.measurements.export module
augur.util_support package
augur.util_support.color_parser module
augur.util_support.color_parser_line module
augur.util_support.node_data module
augur.util_support.node_data_file module
augur.util_support.node_data_reader module
augur.align module
augur.ancestral module
augur.argparse_ module
augur.clades module
augur.debug module
augur.distance module
augur.errors module
augur.export module
augur.export_v1 module
augur.export_v2 module
augur.frequencies module
augur.frequency_estimators module
augur.index module
augur.lbi module
augur.mask module
augur.merge module
augur.parse module
augur.read_file 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.types module
augur.utils module
augur.validate module
augur.validate_export module
augur.version module
augur.write_file module
Authors
Augur
Home
Augur
Developer API
augur package
augur.util_support package
Edit on GitHub
augur.util_support.color_parser module
class
augur.util_support.color_parser.
ColorParser
(
*
,
mapping_filename
,
use_defaults
=
True
)
Bases:
object
property
mapping
parse_file
(
file
)
Read the Docs
v: stable
Versions
latest
stable
26.0.0
25.4.0
25.3.0
25.2.0
25.1.1
25.1.0
25.0.0
24.4.0
24.3.0
24.2.3
24.2.2
24.2.1
24.2.0
24.1.0
24.0.0
23.1.1
23.1.0
23.0.0
22.4.0
22.3.0
22.2.0
22.1.0
22.0.3
22.0.2
22.0.1
22.0.0
21.1.0
21.0.1
21.0.0
20.0.0
19.3.0
19.2.0
19.1.0
19.0.0
18.2.0
18.1.2
18.1.1
18.1.0
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
14.0.0
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
10.2.0
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
5.2.0
5.1.1
5.1.0
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