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Microbial pan-GWAS using the output from Roary

Project Description

Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. It reports a list of genes sorted by strength of association per trait.


  • Python (Tested with versions 2.7 and 3.5)
  • SciPy (Tested with versions 0.16, 0.17, 0.18)

If you supply custom trees (Optional)

  • ete3
  • six

Note that ete3 and six are not automatically installed. You can do pip install ete3 six to get them

Using the GUI (Optional)

  • Tkinter/ttk

Tkinter/ttk is already part of most python distributions. If you lack it consider getting Homebrew/Linuxbrew and running brew install python –with-tcl-tk


The easiest way to install Scoary is through the pip package manager:

pip install scoary


scoary -g <gene_presence_absence.csv> -t <traits.csv>


The most updated documentation for scoary is found at the project site


If you use Scoary, please citing our paper


Scoary is freely available under a GPLv3 license.


Ola Brynildsrud (

Release History

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