---
name: "augur"
section: "1"
platform: "linux"
package: "augur"
version: "24.4.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/augur"
---

# augur(1)

pipeline components for real-time virus analysis

## NAME

augur - pipeline components for real-time virus analysis

## DESCRIPTION

usage: augur \[-h\]

-

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

Augur: A bioinformatics toolkit for phylogenetic analysis.

### 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

## AUTHOR

 This manpage was written by Étienne Mollier for the Debian distribution and can be used for any other usage of the program.