E_Coli

Code to generate Suppl. Table 2, Figure 3 and Supplementary Figure 3 of "Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut" (https://doi.org/10.1038/s41564-022-01286-7)

Contains the data (from https://microbiology.figshare.com/articles/dataset/A_comprehensive_and_high-quality_collection_of_E_coli_genomes_and_their_genes/13270073) as well as custom script used to generate the above mentioned Table and Figures.

This custom script has been tested on the Linux operating system. The following dependencies were used for the paper, though other versions may work:

Python 3.7.6
Python libraries:
    numpy 1.18.1
    Pandas 1.0.3
    bokeh 2.2.3
    ete3 3.1.2
    holoviews 0.11.6