The easiest way to install is through conda, which will also install the dependencies:

conda install poppunk

Then run with poppunk.


PopPUNK requires python3.8 to run (which on many default Linux installations is run using python3 rather than python).

Installing with pip

If you do not have conda, you can also install through pip:

python3 -m pip install poppunk

You will also need mash (v2 or higher) installed (see Dependencies).

Clone the code

You can also clone the github to run the latest version, which is executed by:

git clone && cd PopPUNK

This will also give access to the Scripts.

You will need to install the Dependencies yourself (you can still use conda or pip for this purpose).


We tested PopPUNK with the following packages:

  • python3 (3.8.2)
  • DendroPy (4.3.0)
  • hdbscan (0.8.13)
  • matplotlib (2.1.2)
  • networkx (2.1)
  • numpy (1.14.1)
  • numba (0.36.2)
  • pandas (0.22.0)
  • scikit-learn (0.19.1)
  • scipy (1.0.0)
  • sharedmem (0.3.5)

numba may need gcc >=v4.8 to install correctly through pip (if you are getting OSError or 'GLIBCXX_3.4.17' not found).

You will need a mash installation which is v2.0 or higher

Optionally, you can use rapidnj if producing output with --microreact and --rapidnj options. We used v2.3.2.