Augur
version: 11.1.0
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Table of contents
Installation
Using Augur
Augur subcommands
augur parse
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.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_beast 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
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Index
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Index
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E
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I
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W
A
add() (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)
are_clades_defined() (in module augur.export_v2)
are_dates_defined() (in module augur.export_v2)
are_mutations_defined() (in module augur.export_v2)
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_beast (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)
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_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)
check_arguments() (in module augur.align)
check_duplicates() (in module augur.align)
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)
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_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)
cross_validate() (augur.titer_model.TreeModel method)
D
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)
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)
filter_by_query() (in module augur.filter)
filter_strains() (augur.titer_model.TiterCollection static method)
find_executable() (in module augur.tree)
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)
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)
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_json_name() (in module augur.utils)
get_mutations() (augur.titer_model.SubstitutionModel method)
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)
I
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
is_date_ambiguous() (in module augur.utils)
is_node_in_clade() (in module augur.clades)
is_valid() (in module augur.export_v2)
is_vcf() (in module augur.utils)
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)
mask_fasta() (in module augur.mask)
mask_sites_in_multiple_sequence_alignment() (in module augur.tree)
mask_vcf() (in module augur.mask)
MismatchNodeError
MissingNodeError
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_prop_is_normal_trait() (in module augur.export_v2)
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)
open_file() (in module augur.utils)
P
parse_beast_tree() (in module augur.import_beast)
parse_nexus() (in module augur.import_beast)
parse_node_data_and_metadata() (in module augur.export_v2)
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_what_to_do_next() (in module augur.import_beast)
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
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_titers() (augur.titer_model.TiterCollection method)
read_tree() (in module augur.utils)
read_vcf() (in module augur.filter)
recursively_decorate_tree_json_v1_schema() (in module augur.export_v1)
reference_virus_statistic() (augur.titer_model.TiterModel method)
refine() (in module augur.refine)
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.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)
run() (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)
(in module augur.filter)
(in module augur.frequencies)
(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_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)
show() (augur.validate.ValidationErrors method)
(augur.validate.ValidationWarnings 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)
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)
U
update_deprecated_names() (in module augur.export_v2)
V
valid (augur.frequency_estimators.freq_est_clipped attribute)
validate() (augur.titer_model.TiterModel method)
(in module augur.validate)
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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