Augur
version 26.2.0
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
View page source
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
)