This is an Augur-specific installation guide. If you wish to use Nextstrain as a whole, please refer to the Nextstrain installation guide.

Installing dependencies

Augur uses some external bioinformatics programs:

  • augur align requires mafft

  • augur tree requires at least one of:

  • Bacterial data (or any VCF usage) requires vcftools

If you use Conda or Mamba, you can install them in an active environment:

conda install -c conda-forge -c bioconda mafft raxml fasttree iqtree vcftools --yes

On macOS using Homebrew:

brew tap brewsci/bio
brew install mafft iqtree raxml fasttree vcftools

On Debian/Ubuntu:

sudo apt install mafft iqtree raxml fasttree vcftools

Other Linux distributions will likely have the same packages available, although the names may differ slightly.

Install Augur as a user

Using Mamba

This assumes you have Conda installed and an environment active. If not, refer to instructions for ambient runtime setup on the Nextstrain installation guide.

conda install -c conda-forge -c bioconda augur

If you encounter environment solving errors or want a faster installation process, use mamba as a drop-in replacement for conda:

mamba install -c conda-forge -c bioconda augur

Using pip from PyPi

Augur is written in Python 3 and requires at least Python 3.8. It’s published on PyPi as nextstrain-augur, so you can install it with pip like so:

python3 -m pip install nextstrain-augur

From source

git clone
python3 -m pip install .

This installs Augur along with external Python dependencies.

Install Augur as a developer

python3 -m pip install -e '.[dev]'

This installs dependencies necessary for local development.

Testing if it worked

If installation worked, you should be able to run augur --help and see augur’s primary help output.