Augur
version: 12.1.1
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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
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
»
Index
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
A
add() (augur.filter.PriorityQueue method)
(augur.validate.ValidationWarnings method)
add_core_args() (in module augur.export_v1)
add_default_command() (in module augur)
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)
ambiguous_date_to_date_range() (in module augur.utils)
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)
are_clades_defined() (in module augur.export_v2)
are_dates_defined() (in module augur.export_v2)
are_mutations_defined() (in module augur.export_v2)
assert_only_less_significant_uncertainty() (augur.util_support.date_disambiguator.DateDisambiguator 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.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.util_support (module)
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.utils (module)
augur.validate (module)
augur.validate_export (module)
augur.version (module)
AugurException
auspice_config_v2() (in module augur.validate)
available_cpu_cores() (in module augur.utils)
B
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)
C
calc_confidence() (augur.frequency_estimators.alignment_frequencies method)
(augur.frequency_estimators.tree_frequencies method)
calc_freqs() (augur.frequency_estimators.nested_frequencies method)
calc_tree_dates() (in module augur.import_beast)
calculate_LBI() (in module augur.lbi)
calculate_sequences_per_group() (in module augur.filter)
check_against_tree_file() (augur.util_support.node_data_reader.NodeDataReader method)
check_arguments() (in module augur.align)
check_duplicates() (in module augur.align)
check_metadata_duplicates() (augur.util_support.metadata_file.MetadataFile method)
collapse_colinear_mutations() (augur.titer_model.SubstitutionModel method)
collect_mutations_and_sequences() (in module augur.ancestral)
collect_node_data() (in module augur.import_beast)
(in module augur.refine)
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)
columns() (augur.util_support.metadata_file.MetadataFile property)
command_name() (in module augur)
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)
compute_entropies_for_discrete_traits() (in module augur.import_beast)
configure_warnings() (in module augur.export_v2)
construct_author_info_v1() (in module augur.export_v1)
construct_filters() (in module augur.filter)
construct_mut() (in module augur.translate)
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_queues_by_group() (in module augur.filter)
cross_validate() (augur.titer_model.TreeModel method)
D
DateDisambiguator (class in augur.util_support.date_disambiguator)
deep_add_or_update() (augur.util_support.node_data.NodeData method)
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)
DuplicatedNonDictAttributeError
E
ensure_config_is_v1() (in module augur.export_v1)
ensure_no_duplicate_names() (in module augur.validate_export)
ensure_reference_strain_present() (in module augur.align)
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)
F
fake_alignment() (in module augur.import_beast)
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)
filter_by_date() (in module augur.filter)
filter_by_exclude() (in module augur.filter)
filter_by_exclude_all() (in module augur.filter)
filter_by_exclude_where() (in module augur.filter)
filter_by_non_nucleotide() (in module augur.filter)
filter_by_query() (in module augur.filter)
filter_by_sequence_index() (in module augur.filter)
filter_by_sequence_length() (in module augur.filter)
filter_kwargs_to_str() (in module augur.filter)
filter_strains() (augur.titer_model.TiterCollection static method)
FilterException
find_executable() (in module augur.tree)
find_key_type() (augur.util_support.metadata_file.MetadataFile method)
find_most_recent_tip() (in module augur.import_beast)
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.util_support.date_disambiguator.DateDisambiguator property)
format_frequencies() (in module augur.frequencies)
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)
get_augur_version() (in module augur.utils)
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_genes_from_file() (in module augur.translate)
get_groups_for_subsampling() (in module augur.filter)
get_items() (augur.filter.PriorityQueue method)
get_json_name() (in module augur.utils)
get_mutations() (augur.titer_model.SubstitutionModel method)
get_numerical_date_from_value() (in module augur.utils)
get_numerical_dates() (in module augur.utils)
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_date_offset() (in module augur.import_beast)
get_root_sequence() (in module augur.export_v1)
(in module augur.export_v2)
get_sequence() (in module augur.reconstruct_sequences)
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)
H
hex_code() (augur.util_support.color_parser_line.ColorParserLine property)
I
include() (in module augur.filter)
include_by_include_where() (in module augur.filter)
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
InvalidOption
InvalidTreeError
invoke_command() (augur.util_support.shell_command_runner.ShellCommandRunner method)
is_comment_or_blank() (augur.util_support.color_parser_line.ColorParserLine method)
is_date_ambiguous() (in module augur.utils)
is_generated_by_incompatible_augur() (augur.util_support.node_data_file.NodeDataFile property)
is_node_in_clade() (in module augur.clades)
is_valid() (in module augur.export_v2)
is_vcf() (in module augur.utils)
items() (augur.util_support.node_data_file.NodeDataFile method)
J
json_to_tree() (in module augur.utils)
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.validate)
load_json_schema() (in module augur.validate)
load_mask_sites() (in module augur.utils)
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)
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.util_support.date_disambiguator)
metadata() (augur.util_support.metadata_file.MetadataFile property)
MetadataFile (class in augur.util_support.metadata_file)
MismatchNodeError
MissingNodeError
modified_env() (augur.util_support.shell_command_runner.ShellCommandRunner property)
mugration_inference() (in module augur.traits)
mutation_frequencies() (augur.frequency_estimators.alignment_frequencies method)
myopen() (in module augur.utils)
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_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)
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)
nthreads_value() (in module augur.utils)
numeric_date() (in module augur.filter)
(in module augur.frequencies)
O
obs (augur.frequency_estimators.freq_est_clipped attribute)
P
pair() (augur.util_support.color_parser_line.ColorParserLine method)
parse_beast_tree() (in module augur.import_beast)
parse_file (augur.util_support.metadata_file.MetadataFile attribute)
parse_file() (augur.util_support.color_parser.ColorParser method)
parse_filter_query() (in module augur.filter)
parse_nexus() (in module augur.import_beast)
parse_node_data_and_metadata() (in module augur.export_v2)
parse_sequence() (in module augur.parse)
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_error() (augur.util_support.shell_command_runner.ShellCommandRunner static method)
print_error_message() (augur.util_support.shell_command_runner.ShellCommandRunner method)
print_what_to_do_next() (in module augur.import_beast)
PriorityQueue (class in augur.filter)
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.util_support.date_disambiguator.DateDisambiguator method)
read() (augur.util_support.metadata_file.MetadataFile method)
(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_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.utils)
read_node_data() (in module augur.utils)
read_priority_scores() (in module augur.filter)
read_reference() (in module augur.align)
read_sequences() (in module augur.align)
read_strains() (in module augur.utils)
read_titers() (augur.titer_model.TiterCollection method)
read_tree() (in module augur.utils)
read_vcf() (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.util_support.date_disambiguator.DateDisambiguator property)
register_arguments() (in module augur.align)
(in module augur.ancestral)
(in module augur.clades)
(in module augur.distance)
(in module augur.export)
(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.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)
register_arguments_beast() (in module augur.import_beast)
register_arguments_v1() (in module augur.export_v1)
register_arguments_v2() (in module augur.export_v2)
remove_reference_sequence() (in module augur.align)
resolve_uncertain_int() (in module augur.util_support.date_disambiguator)
run() (augur.titers.infer_substitution_model method)
(augur.titers.infer_tree_model method)
(augur.util_support.shell_command_runner.ShellCommandRunner method)
(in module augur)
(in module augur.align)
(in module augur.ancestral)
(in module augur.clades)
(in module augur.distance)
(in module augur.export)
(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.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_beast() (in module augur.import_beast)
run_shell_command() (in module augur.utils)
run_v1() (in module augur.export_v1)
run_v2() (in module augur.export_v2)
running_average() (in module augur.frequency_estimators)
S
safe_translate() (in module augur.translate)
select_nodes_in_season() (in module augur.lbi)
set_annotations() (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_panels() (in module augur.export_v2)
set_title() (in module augur.export_v2)
shell_args() (augur.util_support.shell_command_runner.ShellCommandRunner property)
shell_executable() (augur.util_support.shell_command_runner.ShellCommandRunner property)
ShellCommandRunner (class in augur.util_support.shell_command_runner)
show() (augur.validate.ValidationErrors method)
(augur.validate.ValidationWarnings method)
signal_from_error() (augur.util_support.shell_command_runner.ShellCommandRunner static method)
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)
summarise_parsed_traits() (in module augur.import_beast)
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.util_support.date_disambiguator)
U
uncertain_date_components() (augur.util_support.date_disambiguator.DateDisambiguator 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.filter)
validate_data_json() (in module augur.export_v2)
validate_json() (in module augur.validate)
ValidateError
ValidationErrors (class in augur.validate)
ValidationWarnings (class in augur.validate)
verifyMainJSONIsInternallyConsistent() (in module augur.validate_export)
verifyMetaAndOrTreeJSONsAreInternallyConsistent() (in module augur.validate_export)
W
warning() (in module augur.export_v2)
write_json() (in module augur.utils)
write_out_informative_fasta() (in module augur.tree)
write_seqs() (in module augur.align)
write_vcf() (in module augur.filter)
write_VCF_translation() (in module augur.utils)
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