Augur
version: 10.0.4
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Table of contents
Installation
Using Augur
Augur Releases & Upgrading
Frequently Asked Questions
Tutorials
Examples of Augur in the wild
Python Development API
Authors
Augur
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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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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.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_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)
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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