Augur
development version
(
430a9766
)
Table of contents
Installation
Using Augur
Augur subcommands
augur parse
augur curate
normalize-strings
titlecase
format-dates
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
Deprecated features
Augur v6 Release Notes
Migrating from augur v5 to v6
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
Home
Augur
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Index
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C
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D
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W
A
add() (augur.filter.subsample.PriorityQueue method)
add_core_args() (in module augur.export_v1)
add_option_args() (in module augur.export_v1)
add_tsv_metadata_to_nodes() (in module augur.export_v1)
add_version_alias() (in module augur)
alignment_frequencies (class in augur.frequency_estimators)
AlignmentError
AlignmentKdeFrequencies (class in augur.frequency_estimators)
AmbiguousDate (class in augur.dates.ambiguous_date)
analyse_insertions() (in module augur.align)
ancestral_sequence_inference() (in module augur.ancestral)
annotate_parents_for_tree() (in module augur.utils)
annotate_strains() (in module augur.sequence_traits)
annotate_strains_by_gene() (in module augur.sequence_traits)
annotate_tree() (augur.titer_model.SubstitutionModel method)
annotations (augur.util_support.node_data_file.NodeDataFile property)
apply_filters() (in module augur.filter.include_exclude_rules)
are_mutations_defined() (in module augur.export_v2)
ArgparseEnum (class in augur.types)
argtype() (augur.types.ArgparseEnum class method)
as_json() (in module augur.io.json)
assert_only_less_significant_uncertainty() (augur.dates.ambiguous_date.AmbiguousDate method)
assign_aa_fasta() (in module augur.translate)
assign_aa_vcf() (in module augur.translate)
assign_clades() (in module augur.clades)
assign_titers() (augur.titer_model.TiterModel method)
attach_features() (in module augur.sequence_traits)
augur
module
augur.align
module
augur.ancestral
module
augur.clades
module
augur.dates
module
augur.dates.ambiguous_date
module
augur.dates.errors
module
augur.distance
module
augur.errors
module
augur.export
module
augur.export_v1
module
augur.export_v2
module
augur.filenames
module
augur.filter
module
augur.filter._run
module
augur.filter.include_exclude_rules
module
augur.filter.io
module
augur.filter.subsample
module
augur.filter.validate_arguments
module
augur.frequencies
module
augur.frequency_estimators
module
augur.import_
module
augur.index
module
augur.io
module
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.vcf
module
augur.lbi
module
augur.mask
module
augur.measurements
module
augur.measurements.concat
module
augur.measurements.export
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.types
module
augur.util_support
module
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.utils
module
augur.validate
module
augur.validate_export
module
augur.version
module
AugurError
AugurJSONEncoder (class in augur.utils)
auspice_config_v2() (in module augur.validate)
available_cpu_cores() (in module augur.utils)
B
branches (augur.util_support.node_data_file.NodeDataFile property)
build_fasttree() (in module augur.tree)
build_iqtree() (in module augur.tree)
build_node_data() (augur.util_support.node_data_reader.NodeDataReader method)
build_raxml() (in module augur.tree)
BytesWrittenCounterIO (class in augur.utils)
C
calc_confidence() (augur.frequency_estimators.alignment_frequencies method)
(augur.frequency_estimators.tree_frequencies method)
calc_freqs() (augur.frequency_estimators.nested_frequencies method)
calculate_LBI() (in module augur.lbi)
calculate_sequences_per_group() (in module augur.filter.subsample)
check_against_tree_file() (augur.util_support.node_data_reader.NodeDataReader method)
check_arg_combinations() (in module augur.translate)
check_arguments() (in module augur.align)
check_conflicting_args() (in module augur.tree)
check_duplicates() (in module augur.align)
cleanup_outputs() (in module augur.filter.io)
collapse_colinear_mutations() (augur.titer_model.SubstitutionModel method)
collect_mutations() (in module augur.ancestral)
collect_node_data() (in module augur.refine)
collect_sequences() (in module augur.ancestral)
collectAAMutationGenesV1() (in module augur.validate_export)
collectBranchLabels() (in module augur.validate_export)
collectMutationGenes() (in module augur.validate_export)
collectTreeAttrsV1() (in module augur.validate_export)
collectTreeAttrsV2() (in module augur.validate_export)
ColorParser (class in augur.util_support.color_parser)
ColorParserLine (class in augur.util_support.color_parser_line)
column_type_pair() (in module augur.filter.io)
columns (augur.io.metadata.Metadata attribute)
compile_potencies() (augur.titer_model.TiterModel method)
compile_substitution_effects() (augur.titer_model.SubstitutionModel method)
compile_titers() (augur.titer_model.TiterModel method)
compile_virus_effects() (augur.titer_model.TiterModel method)
configure_warnings() (in module augur.export_v2)
ConflictingArgumentsException
construct_author_info_v1() (in module augur.export_v1)
construct_filters() (in module augur.filter.include_exclude_rules)
construct_mut() (in module augur.translate)
CONTEXT_LENGTH (augur.io.json.JSONDecodeError attribute)
contextualize_char() (in module augur.io.json)
convert_tree_to_json_structure() (in module augur.export_v1)
(in module augur.export_v2)
count_observations() (in module augur.frequency_estimators)
count_strains() (augur.titer_model.TiterCollection static method)
counter_to_disambiguation_suffix() (in module augur.export_v2)
create_author_data() (in module augur.export_v2)
create_branch_labels() (in module augur.export_v2)
create_branch_mutations() (in module augur.export_v2)
create_mask() (in module augur.ancestral)
create_queues_by_group() (in module augur.filter.subsample)
cross_validate() (augur.titer_model.TreeModel method)
CustomOrderedDict (class in augur.export_v2)
D
DataErrorMethod (class in augur.types)
deep_add_or_update() (augur.util_support.node_data.NodeData method)
default() (augur.io.json.JsonEncoder method)
(augur.utils.AugurJSONEncoder method)
delimiter (augur.io.metadata.Metadata attribute)
deprecated() (in module augur.export_v2)
determine_autologous_titers() (augur.titer_model.TiterCollection method)
determine_relevant_mutations() (augur.titer_model.SubstitutionModel method)
dtps (augur.frequency_estimators.freq_est_clipped attribute)
dump_ndjson() (in module augur.io.json)
DuplicatedNonDictAttributeError
E
elide_path() (in module augur.validate)
EmptyOutputReportingMethod (class in augur.types)
ensure_config_is_v1() (in module augur.export_v1)
ensure_no_duplicate_names() (in module augur.validate_export)
ensure_no_multiple_mutations() (in module augur.clades)
ensure_reference_strain_present() (in module augur.align)
ERROR (augur.types.EmptyOutputReportingMethod attribute)
(augur.types.ValidationMode attribute)
ERROR_ALL (augur.types.DataErrorMethod attribute)
ERROR_FIRST (augur.types.DataErrorMethod attribute)
estimate() (augur.frequency_estimators.AlignmentKdeFrequencies method)
(augur.frequency_estimators.TreeKdeFrequencies method)
estimate_clade_frequencies() (augur.frequency_estimators.tree_frequencies method)
estimate_frequencies() (augur.frequency_estimators.KdeFrequencies class method)
estimate_genotype_frequency() (augur.frequency_estimators.alignment_frequencies method)
estimate_tip_frequencies_to_proportion() (augur.frequency_estimators.TreeKdeFrequencies method)
export_v1() (in module augur.validate)
export_v2() (in module augur.validate)
extract_variables() (in module augur.filter.include_exclude_rules)
F
fatal() (in module augur.export_v2)
(in module augur.validate)
fe (augur.frequency_estimators.freq_est_clipped attribute)
fields (augur.util_support.color_parser_line.ColorParserLine property)
filter_by_ambiguous_date() (in module augur.filter.include_exclude_rules)
filter_by_exclude() (in module augur.filter.include_exclude_rules)
filter_by_exclude_all() (in module augur.filter.include_exclude_rules)
filter_by_exclude_where() (in module augur.filter.include_exclude_rules)
filter_by_max_date() (in module augur.filter.include_exclude_rules)
filter_by_max_length() (in module augur.filter.include_exclude_rules)
filter_by_min_date() (in module augur.filter.include_exclude_rules)
filter_by_min_length() (in module augur.filter.include_exclude_rules)
filter_by_non_nucleotide() (in module augur.filter.include_exclude_rules)
filter_by_query() (in module augur.filter.include_exclude_rules)
filter_by_sequence_index() (in module augur.filter.include_exclude_rules)
filter_strains() (augur.titer_model.TiterCollection static method)
find_executable() (in module augur.tree)
find_titer_splits() (augur.titer_model.TreeModel method)
first_line() (in module augur.utils)
fit_func() (augur.titer_model.TiterModel method)
fit_l1reg() (augur.titer_model.TiterModel method)
fit_nnl1reg() (augur.titer_model.TiterModel method)
fit_nnl2reg() (augur.titer_model.TiterModel method)
fit_nnls() (augur.titer_model.TiterModel method)
fix_dates() (in module augur.parse)
fix_freq() (in module augur.frequency_estimators)
float_to_datestring() (in module augur.frequency_estimators)
fmt_components (augur.dates.ambiguous_date.AmbiguousDate property)
force_include_strains() (in module augur.filter.include_exclude_rules)
force_include_where() (in module augur.filter.include_exclude_rules)
format_frequencies() (in module augur.frequencies)
format_path() (in module augur.validate)
freq_est_clipped (class in augur.frequency_estimators)
frequency_estimator (class in augur.frequency_estimators)
from_json() (augur.frequency_estimators.KdeFrequencies class method)
G
generate_alignment_cmd() (in module augur.align)
generated_by (augur.util_support.node_data_file.NodeDataFile property)
genome_features_to_auspice_annotation() (in module augur.utils)
get_additional_metadata_columns() (in module augur.export_v2)
get_augur_version() (in module augur.utils)
get_bounds() (in module augur.dates.ambiguous_date)
get_chrom_name() (in module augur.mask)
get_config() (in module augur.export_v2)
get_config_colorings_as_dict() (in module augur.export_v2)
get_densities_for_observations() (augur.frequency_estimators.KdeFrequencies class method)
get_density_for_observation() (augur.frequency_estimators.KdeFrequencies class method)
get_distance_between_nodes() (in module augur.distance)
get_distances_to_all_pairs() (in module augur.distance)
get_distances_to_last_ancestor() (in module augur.distance)
get_distances_to_root() (in module augur.distance)
get_groups_for_subsampling() (in module augur.filter.subsample)
get_iso_year_week() (in module augur.dates)
get_items() (augur.filter.subsample.PriorityQueue method)
get_json_name() (in module augur.utils)
get_mutations() (augur.titer_model.SubstitutionModel method)
get_numerical_date_from_value() (in module augur.dates)
get_numerical_dates() (in module augur.dates)
get_params() (augur.frequency_estimators.KdeFrequencies method)
get_parent_name_by_child_name_for_tree() (in module augur.utils)
get_path_no_terminals() (augur.titer_model.TreeModel method)
get_pivots() (in module augur.frequency_estimators)
get_reference_sequence_from_root_node() (in module augur.clades)
get_root_sequence() (in module augur.export_v1)
get_sequence() (in module augur.reconstruct_sequences)
get_unique_keys() (in module augur.validate)
get_useful_metadata_columns() (in module augur.filter.io)
get_values_across_nodes() (in module augur.export_v2)
good_pivots (augur.frequency_estimators.freq_est_clipped attribute)
good_tps (augur.frequency_estimators.freq_est_clipped attribute)
grouped() (in module augur.validate)
H
hex_code (augur.util_support.color_parser_line.ColorParserLine property)
I
id_column (augur.io.metadata.Metadata attribute)
index_sequence() (in module augur.index)
index_sequences() (in module augur.index)
index_vcf() (in module augur.index)
infer_substitution_model (class in augur.titers)
infer_tree_model (class in augur.titers)
initial_guess() (augur.frequency_estimators.frequency_estimator method)
InsufficientDataException
InvalidDate
InvalidDelimiter
InvalidOption
InvalidTreeError
InvalidYearBounds
invoke_command() (augur.io.shell_command_runner.ShellCommandRunner method)
is_comment_or_blank() (augur.util_support.color_parser_line.ColorParserLine method)
is_date_ambiguous() (in module augur.dates)
is_generated_by_incompatible_augur (augur.util_support.node_data_file.NodeDataFile property)
is_node_attr_defined() (in module augur.export_v2)
is_node_in_clade() (in module augur.clades)
is_valid() (in module augur.export_v2)
is_vcf() (in module augur.io.vcf)
items() (augur.util_support.node_data_file.NodeDataFile method)
J
json_size() (in module augur.utils)
json_to_tree() (in module augur.utils)
JSONDecodeError
JsonEncoder (class in augur.io.json)
K
KdeFrequencies (class in augur.frequency_estimators)
L
learn() (augur.frequency_estimators.freq_est_clipped method)
(augur.frequency_estimators.frequency_estimator method)
load_alignments() (in module augur.reconstruct_sequences)
load_features() (in module augur.utils)
load_from_file() (augur.titer_model.TiterCollection static method)
load_json() (in module augur.io.json)
(in module augur.validate)
load_json_schema() (in module augur.validate)
load_mask_sites() (in module augur.utils)
load_ndjson() (in module augur.io.json)
logit_inv() (in module augur.frequency_estimators)
logit_transform() (in module augur.frequency_estimators)
M
make_gaps_ambiguous() (in module augur.align)
make_parser() (in module augur)
make_pivots() (in module augur.frequency_estimators)
make_seqgraph() (augur.titer_model.SubstitutionModel method)
make_training_set() (augur.titer_model.TiterModel method)
make_treegraph() (augur.titer_model.TreeModel method)
mapping (augur.util_support.color_parser.ColorParser property)
mark_char() (in module augur.io.json)
mask_fasta() (in module augur.mask)
mask_sequence() (in module augur.mask)
mask_sites_in_multiple_sequence_alignment() (in module augur.tree)
mask_vcf() (in module augur.mask)
max_day_for_year_month() (in module augur.dates.ambiguous_date)
measurements() (in module augur.validate)
measurements_collection_config() (in module augur.validate)
Metadata (class in augur.io.metadata)
MismatchNodeError
MissingNodeError
modified_env (augur.io.shell_command_runner.ShellCommandRunner property)
module
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
move_to_end_if_present() (augur.export_v2.CustomOrderedDict method)
mugration_inference() (in module augur.traits)
mutation_frequencies() (augur.frequency_estimators.alignment_frequencies method)
N
nested_frequencies (class in augur.frequency_estimators)
node_data_files (augur.util_support.node_data_reader.NodeDataReader property)
node_data_prop_is_normal_trait() (in module augur.export_v2)
node_div() (in module augur.export_v2)
node_names_from_tree_file (augur.util_support.node_data_reader.NodeDataReader property)
NodeData (class in augur.util_support.node_data)
NodeDataFile (class in augur.util_support.node_data_file)
NodeDataObject (class in augur.util_support.node_data_file)
NodeDataReader (class in augur.util_support.node_data_reader)
nodes (augur.util_support.node_data_file.NodeDataFile property)
normalize() (augur.titer_model.TiterCollection method)
normalize_titers() (augur.titer_model.TiterCollection method)
normalize_to_frequencies() (augur.frequency_estimators.KdeFrequencies class method)
NoVariationError
nthreads_value() (in module augur.utils)
numeric_date() (in module augur.dates)
numeric_date_type() (in module augur.dates)
O
obs (augur.frequency_estimators.freq_est_clipped attribute)
open() (augur.io.metadata.Metadata method)
open_file() (in module augur.io)
(in module augur.io.file)
orderKeys() (in module augur.export_v2)
P
pair() (augur.util_support.color_parser_line.ColorParserLine method)
parse_file() (augur.util_support.color_parser.ColorParser method)
parse_filter_query() (in module augur.filter.include_exclude_rules)
parse_genes_argument() (in module augur.utils)
parse_node_data_and_metadata() (in module augur.export_v2)
parse_nodes() (in module augur.clades)
parse_sequence() (in module augur.parse)
path (augur.io.metadata.Metadata attribute)
pivot_freq (augur.frequency_estimators.freq_est_clipped attribute)
pivot_lower_cutoff (augur.frequency_estimators.freq_est_clipped attribute)
pivot_upper_cutoff (augur.frequency_estimators.freq_est_clipped attribute)
pivots (augur.frequency_estimators.freq_est_clipped attribute)
postprocess() (in module augur.align)
pq() (in module augur.frequency_estimators)
predict_titer() (augur.titer_model.SubstitutionModel method)
(augur.titer_model.TreeModel method)
prepare() (augur.frequency_estimators.tree_frequencies method)
(augur.titer_model.SubstitutionModel method)
(augur.titer_model.TreeModel method)
(in module augur.align)
prepare_tree() (augur.titer_model.TreeModel method)
prettify() (in module augur.parse)
prettify_alignment() (in module augur.align)
print_err() (in module augur.io.print)
print_error() (augur.io.shell_command_runner.ShellCommandRunner static method)
print_error_message() (augur.io.shell_command_runner.ShellCommandRunner method)
PriorityQueue (class in augur.filter.subsample)
process_annotations() (in module augur.export_v1)
process_colorings() (in module augur.export_v1)
process_geographic_info() (in module augur.export_v1)
process_panels() (in module augur.export_v1)
prune_seqs_matching_alignment() (in module augur.align)
R
range() (augur.dates.ambiguous_date.AmbiguousDate method)
read() (augur.util_support.node_data_reader.NodeDataReader method)
read_alignment() (in module augur.align)
read_bed_file() (in module augur.utils)
read_colors() (in module augur.utils)
read_config() (in module augur.utils)
read_distance_map() (in module augur.distance)
read_entries() (in module augur.utils)
read_in_clade_definitions() (in module augur.clades)
read_in_features() (in module augur.sequence_traits)
read_in_translate_vcf() (in module augur.sequence_traits)
read_lat_longs() (in module augur.utils)
read_mask_file() (in module augur.utils)
read_metadata() (in module augur.io)
(in module augur.io.metadata)
read_metadata_with_sequences() (in module augur.io.metadata)
read_node_data() (in module augur.utils)
read_priority_scores() (in module augur.filter.io)
read_reference() (in module augur.align)
read_sequences() (in module augur.align)
(in module augur.io)
(in module augur.io.sequences)
read_strains() (in module augur.io)
(in module augur.utils)
read_table_to_dict() (in module augur.io.metadata)
read_titers() (augur.titer_model.TiterCollection method)
read_tree() (in module augur.utils)
recursively_decorate_tree_json_v1_schema() (in module augur.export_v1)
reference_virus_statistic() (augur.titer_model.TiterModel method)
refine() (in module augur.refine)
regex (augur.dates.ambiguous_date.AmbiguousDate property)
register_arguments() (in module augur.align)
(in module augur.filter)
(in module augur.mask)
register_parser() (in module augur.align)
(in module augur.ancestral)
(in module augur.clades)
(in module augur.distance)
(in module augur.export)
(in module augur.export_v1)
(in module augur.export_v2)
(in module augur.filter)
(in module augur.frequencies)
(in module augur.import_)
(in module augur.index)
(in module augur.lbi)
(in module augur.mask)
(in module augur.measurements)
(in module augur.measurements.concat)
(in module augur.measurements.export)
(in module augur.parse)
(in module augur.reconstruct_sequences)
(in module augur.refine)
(in module augur.sequence_traits)
(in module augur.titers)
(in module augur.traits)
(in module augur.translate)
(in module augur.tree)
(in module augur.validate)
(in module augur.version)
remove_reference_sequence() (in module augur.align)
resolve_uncertain_int() (in module augur.dates.ambiguous_date)
rows() (augur.io.metadata.Metadata method)
run() (augur.io.shell_command_runner.ShellCommandRunner method)
(augur.titers.infer_substitution_model method)
(augur.titers.infer_tree_model method)
(in module augur)
(in module augur.align)
(in module augur.ancestral)
(in module augur.clades)
(in module augur.distance)
(in module augur.export_v1)
(in module augur.export_v2)
(in module augur.filter)
(in module augur.filter._run)
(in module augur.frequencies)
(in module augur.index)
(in module augur.lbi)
(in module augur.mask)
(in module augur.measurements.concat)
(in module augur.measurements.export)
(in module augur.parse)
(in module augur.reconstruct_sequences)
(in module augur.refine)
(in module augur.sequence_traits)
(in module augur.traits)
(in module augur.translate)
(in module augur.tree)
(in module augur.validate)
(in module augur.version)
run_ancestral() (in module augur.ancestral)
run_shell_command() (in module augur.io.shell_command_runner)
running_average() (in module augur.frequency_estimators)
S
safe_translate() (in module augur.translate)
select_nodes_in_season() (in module augur.lbi)
sequences_json() (in module augur.translate)
sequences_vcf() (in module augur.translate)
set_annotations() (in module augur.export_v2)
set_branch_attrs_on_tree() (in module augur.export_v2)
set_build_url() (in module augur.export_v2)
set_colorings() (in module augur.export_v2)
set_data_provenance() (in module augur.export_v2)
set_description() (in module augur.export_v2)
set_display_defaults() (in module augur.export_v2)
set_filters() (in module augur.export_v2)
set_geo_resolutions() (in module augur.export_v2)
set_maintainers() (in module augur.export_v2)
set_node_attrs_on_tree() (in module augur.export_v2)
set_order() (augur.export_v2.CustomOrderedDict method)
set_panels() (in module augur.export_v2)
set_title() (in module augur.export_v2)
shell_args (augur.io.shell_command_runner.ShellCommandRunner property)
shell_executable (augur.io.shell_command_runner.ShellCommandRunner property)
ShellCommandRunner (class in augur.io.shell_command_runner)
shorten_as_json() (in module augur.io.json)
shorten_left() (in module augur.io.json)
signal_from_error() (augur.io.shell_command_runner.ShellCommandRunner static method)
SILENT (augur.types.DataErrorMethod attribute)
(augur.types.EmptyOutputReportingMethod attribute)
SKIP (augur.types.ValidationMode attribute)
skip_group_by_with_ambiguous_day() (in module augur.filter.include_exclude_rules)
skip_group_by_with_ambiguous_month() (in module augur.filter.include_exclude_rules)
skip_group_by_with_ambiguous_year() (in module augur.filter.include_exclude_rules)
stiffLH() (augur.frequency_estimators.frequency_estimator method)
strain_census() (augur.titer_model.TiterCollection method)
strip_non_reference() (in module augur.align)
SubstitutionModel (class in augur.titer_model)
T
test_nested_estimator() (in module augur.frequency_estimators)
test_simple_estimator() (in module augur.frequency_estimators)
timestamp_to_float() (in module augur.frequency_estimators)
tip_passes_filters() (augur.frequency_estimators.TreeKdeFrequencies method)
titer_stats() (augur.titer_model.TiterModel method)
TiterCollection (class in augur.titer_model)
TiterModel (class in augur.titer_model)
to_json() (augur.frequency_estimators.KdeFrequencies method)
TooManyGroupsError
tps (augur.frequency_estimators.freq_est_clipped attribute)
train() (augur.titer_model.SubstitutionModel method)
(augur.titer_model.TreeModel method)
trait (augur.util_support.color_parser_line.ColorParserLine property)
trait_value (augur.util_support.color_parser_line.ColorParserLine property)
translate_feature() (in module augur.translate)
translate_vcf_feature() (in module augur.translate)
tree_frequencies (class in augur.frequency_estimators)
tree_layout() (in module augur.export_v1)
TreeKdeFrequencies (class in augur.frequency_estimators)
TreeKdeFrequenciesError
TreeModel (class in augur.titer_model)
tuple_to_date() (in module augur.dates.ambiguous_date)
U
uncertain_date_components (augur.dates.ambiguous_date.AmbiguousDate property)
update() (augur.util_support.node_data.NodeData method)
update_deprecated_names() (in module augur.export_v2)
V
valid (augur.frequency_estimators.freq_est_clipped attribute)
validate() (augur.titer_model.TiterModel method)
(augur.util_support.node_data_file.NodeDataFile method)
(in module augur.validate)
validate_arguments() (in module augur.ancestral)
(in module augur.filter.validate_arguments)
validate_collection_config_fields() (in module augur.validate)
validate_collection_display_defaults() (in module augur.validate)
validate_data_json() (in module augur.export_v2)
validate_json() (in module augur.validate)
validate_measurements_config() (in module augur.validate)
ValidateError
validation_failure() (in module augur.export_v2)
ValidationMode (class in augur.types)
verifyMainJSONIsInternallyConsistent() (in module augur.validate_export)
verifyMetaAndOrTreeJSONsAreInternallyConsistent() (in module augur.validate_export)
W
WARN (augur.types.DataErrorMethod attribute)
(augur.types.EmptyOutputReportingMethod attribute)
(augur.types.ValidationMode attribute)
warn_if_clades_not_found() (in module augur.clades)
warning() (in module augur.export_v2)
write() (augur.utils.BytesWrittenCounterIO method)
write_json() (in module augur.utils)
write_metadata_based_outputs() (in module augur.filter.io)
write_out_informative_fasta() (in module augur.tree)
write_records_to_fasta() (in module augur.io.sequences)
write_records_to_tsv() (in module augur.io.metadata)
write_seqs() (in module augur.align)
write_sequences() (in module augur.io)
(in module augur.io.sequences)
write_vcf() (in module augur.io.vcf)
write_VCF_translation() (in module augur.io.vcf)
written (augur.utils.BytesWrittenCounterIO attribute)
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