Empress

Empress is a fast and scalable phylogenetic tree viewer.

Installation

Installing Empress "Standalone"

To install the current development version, we recommend creating a new conda environment:

conda create -n empress python=3.6 numpy scipy pandas cython
conda activate empress
conda install -c bioconda scikit-bio biom-format
pip install git+https://github.com/biocore/empress.git

Installing Empress through QIIME 2

Before following these instructions, make sure your QIIME 2 conda environment is activated (a version of at least 2019.1 is required). Then, run the following commands:

pip install git+https://github.com/biocore/empress.git
qiime dev refresh-cache
qiime empress

If you see information about Empress' QIIME 2 plugin, the installation was successful!

Example: Using Empress in QIIME 2

Empress can visualize Phylogeny[Rooted] QIIME 2 artifacts. We're going to use data from the QIIME 2 Moving Pictures Tutorial:

Input Artifacts and Metadata

• rooted-tree.qza view | download
• table.qza view | download
• taxonomy.qza view | download
• sample_metadata.tsv download

Once you've got the above files downloaded into a single directory, run the following command:

qiime empress plot \
    --i-tree rooted-tree.qza \
    --i-feature-table table.qza \
    --m-sample-metadata-file sample_metadata.tsv \
    --m-feature-metadata-file taxonomy.qza \
    --o-visualization empress-tree.qzv

Output Artifacts

• empress-tree.qzv view | download

This QIIME 2 visualization can be viewed either using qiime tools view or by uploading it to view.qiime2.org.

Screenshot

Running Empress' Tests

Please see the tests/README.md file for instructions on how to run Empress' tests.

Acknowledgements

This work is supported by IBM Research AI through the AI Horizons Network. For more information visit the IBM AI Horizons Network website.

Empress' JavaScript code is distributed with the source code of various third-party dependencies (in the empress/support_files/vendor/ directory). Please see DEPENDENCY_LICENSES.md for copies of these dependencies' licenses.