Co-occurrence paper supplement

This repository contains all the data and code require to generate all the figures in the following paper:

Machado D. et al, Polarization of microbial communities in the competition-cooperation trade-off landscape (in preparation)

Usage

Please run download.sh to download and extract larger data files that cannot be hosted in github.
All the figures in the paper can be reproduced by running the respective jupyter notebook.

Tools

HiOrCo: computing higher-order co-occurrence species sets.
CarveMe: reconstruction of genome-scale metabolic models.
SMETANA: simulating cross-feeding interactions in microbial communities.