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Emperor is a python package hosted in GitHub that relies on NumPy, scikit-bio and qcli.

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To clone the git repository directly into your machine:

git clone git://


To perform a global installation of Emperor, execute the following command from a terminal session:

python install

If you do not want to do a global installation, you will have to add the Emperor scripts and libraries to the PATH and PYTHONPATH environment variables. To add these variables to your .bash_profile issue the following terminal commands:

echo "export PATH=$HOME/emperor_bin/:$PATH" >> ~/.bash_profile
echo "export PYTHONPATH=$HOME/emperor_lib/:$PYTHONPATH" >> ~/.bash_profile
python install --install-scripts=~/emperor_bin/ --install-purelib=~/emperor_lib/ --install-lib=~/emperor_lib/

Alternatively Emperor can be installed from the Python Package Index (PyPi) using either conda (note that this method will be notably faster):

conda install scikit-bio
pip install emperor

or using pip:

pip install numpy
pip install emperor

Verifying your installation

To test for a correct installation, open a new terminal window and issue the following command to see the help of -h
Usage: [options] {-i/--input_coords INPUT_COORDS -m/--map_fp MAP_FP}

[] indicates optional input (order unimportant)
{} indicates required input (order unimportant)

This script automates the creation  of three-dimensional PCoA plots to be visualized with Emperor using Google Chrome.

Example usage: 
Print help message and exit -h