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

conda install poppunk

Then run with poppunk.


From v2.1.0 onwards, PopPUNK requires python3.8 to run (which on many default Linux installations is run using python3 rather than python).


From v2.1.2 onwards, PopPUNK no longer supports mash. If you want to use older databases created with mash, please downgrade to <v2

Installing with pip

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

python3 -m pip install poppunk

This may not deal with all necessary 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).


This documentation refers to a conda installation with the following packages:

  • python3 (3.8.2)
  • pp-sketchlib (1.6.2)
  • DendroPy (4.3.0)
  • hdbscan (0.8.13)
  • matplotlib (2.1.2)
  • graph-tool (2.31)
  • numpy (1.14.1)
  • pandas (0.22.0)
  • scikit-learn (0.19.1)
  • scipy (1.0.0)
  • sharedmem (0.3.5)

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