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Augur uses some external bioinformatics programs that are not available on PyPI:
- ``augur align`` requires `mafft <https://mafft.cbrc.jp/alignment/software/>`__
- ``augur tree`` requires at least one of:
- `IQ-TREE <http://www.iqtree.org/>`__ (used by default)
- `RAxML <https://sco.h-its.org/exelixis/web/software/raxml/>`__ (optional alternative)
- `FastTree <http://www.microbesonline.org/fasttree/>`__ (optional alternative)
- Bacterial data (or any VCF usage) requires `vcftools <https://vcftools.github.io/>`__
If you use Conda, you can install them in an active environment:
.. code:: bash
conda install -c conda-forge -c bioconda mafft raxml fasttree iqtree vcftools --yes
On macOS using `Homebrew <https://brew.sh/>`__:
.. code:: bash
brew tap brewsci/bio
brew install mafft iqtree raxml fasttree vcftools
On Debian/Ubuntu:
.. code:: bash
sudo apt install mafft iqtree raxml fasttree vcftools
Other Linux distributions will likely have the same packages available, although the names may differ slightly.
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