positional arguments:

{parse, index, filter, mask, align, tree, refine, ancestral, translate, reconstruct-sequences, clades, traits, sequence-traits, lbi, distance, titers, frequencies, export, validate, version, import, measurements}

parse

Parse delimited fields from FASTA sequence names into a TSV and FASTA file.

index

Count occurrence of bases in a set of sequences.

filter

Filter and subsample a sequence set.

mask

Mask specified sites from a VCF or FASTA file.

align

Align multiple sequences from FASTA.

tree

Build a tree using a variety of methods.

refine

Refine an initial tree using sequence metadata.

ancestral

Infer ancestral sequences based on a tree.

translate

Translate gene regions from nucleotides to amino acids.

reconstruct-sequences

Reconstruct alignments from mutations inferred on the tree

clades

Assign clades to nodes in a tree based on amino-acid or nucleotide signatures.

traits

Infer ancestral traits based on a tree.

sequence-traits

Annotate sequences based on amino-acid or nucleotide signatures.

lbi

Calculate LBI for a given tree and one or more sets of parameters.

distance

Calculate the distance between sequences across entire genes or at a predefined subset of sites.

titers

Annotate a tree with actual and inferred titer measurements.

frequencies

infer frequencies of mutations or clades

export

Export JSON files suitable for visualization with auspice.

validate

Validate files related to augur consumption or export.

version

Print the version of augur.

import

Import analyses into augur pipeline from other systems

measurements

Create JSON files suitable for visualization within the measurements panel of Auspice.

options:

-h, --help

show this help message and exit