augur
5.1.0
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Installation
Command-line usage
Python API
Authors
augur
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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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V
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W
A
add_default_command() (in module augur)
add_metadata_to_tree() (in module augur.export)
add_tsv_metadata_to_nodes() (in module augur.export)
add_version_alias() (in module augur)
alignment_frequencies (class in augur.frequency_estimators)
AlignmentKdeFrequencies (class in augur.frequency_estimators)
ambiguous_date_to_date_range() (in module augur.utils)
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)
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.filenames (module)
augur.filter (module)
augur.frequencies (module)
augur.frequency_estimators (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.version (module)
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)
calculate_LBI() (in module augur.lbi)
checkSchemaIsValid() (in module augur.validate)
collapse_colinear_mutations() (augur.titer_model.SubstitutionModel method)
collect_node_data() (in module augur.refine)
collect_sequences_and_mutations() (in module augur.ancestral)
collect_strain_info() (in module augur.export)
collectAAMutationGenesNextfluSchema() (in module augur.validate)
collectMutationGenes() (in module augur.validate)
collectTreeAttrs() (in module augur.validate)
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)
construct_author_info_and_make_keys() (in module augur.export)
construct_author_info_nexflu() (in module augur.export)
construct_mut() (in module augur.translate)
convert_tree_to_json_structure() (in module augur.export)
count_observations() (in module augur.frequency_estimators)
count_strains() (augur.titer_model.TiterCollection static method)
cross_validate() (augur.titer_model.TreeModel method)
D
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
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)
F
fe (augur.frequency_estimators.freq_est_clipped attribute)
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)
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
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_mask_sites() (in module augur.mask)
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_sequence() (in module augur.export)
get_sequence() (in module augur.reconstruct_sequences)
get_traits() (in module augur.export)
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
is_node_in_clade() (in module augur.clades)
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_excluded_sites() (in module augur.tree)
load_features() (in module augur.utils)
load_from_file() (augur.titer_model.TiterCollection static method)
loadJSONsToValidate() (in module augur.validate)
loadSchemas() (in module augur.validate)
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_sites_in_multiple_sequence_alignment() (in module augur.tree)
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)
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)
O
obs (augur.frequency_estimators.freq_est_clipped attribute)
P
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)
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)
prepare_tree() (augur.titer_model.TreeModel method)
process_annotations() (in module augur.export)
process_colorings() (in module augur.export)
process_geographic_info() (in module augur.export)
process_panels() (in module augur.export)
R
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_metadata() (in module augur.utils)
read_node_data() (in module augur.utils)
read_priority_scores() (in module augur.filter)
read_titers() (augur.titer_model.TiterCollection method)
read_vcf() (in module augur.filter)
recursively_decorate_tree_json_nextflu_schema() (in module augur.export)
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)
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_shell_command() (in module augur.utils)
running_average() (in module augur.frequency_estimators)
S
safe_translate() (in module augur.translate)
select_nodes_in_season() (in module augur.lbi)
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)
tps (augur.frequency_estimators.freq_est_clipped attribute)
train() (augur.titer_model.SubstitutionModel method)
(augur.titer_model.TreeModel method)
transfer_metadata_to_strains() (in module augur.export)
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)
TreeKdeFrequencies (class in augur.frequency_estimators)
TreeModel (class in augur.titer_model)
V
valid (augur.frequency_estimators.freq_est_clipped attribute)
validate() (augur.titer_model.TiterModel method)
ValidateError
verifyMainJSONIsInternallyConsistent() (in module augur.validate)
verifyMetaAndOrTreeJSONsAreInternallyConsistent() (in module augur.validate)
W
write_json() (in module augur.utils)
write_out_informative_fasta() (in module augur.tree)
write_vcf() (in module augur.filter)
write_VCF_translation() (in module augur.utils)
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