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.