PopCOGenT

Purpose

Identifying microbial populations using networks of horizontal gene transfer.

Dependencies

All modules

• A linux-based system (N.B., we are working on a way to get all the dependencies working properly on OSX, but as of now OSX is not a supported operating system).
• Miniconda with python 3.7

The required python and (most) R packages can be installed by creating a conda environment with the included PopCOGenT.yml file as follows:

conda env create -f PopCOGenT.yml

PopCOGenT

• mugsy version 1.2.3
• Infomap

Flexible genome sweep identification

• mmseqs2
• muscle 3.8.31

Core genome sweep identification

• phyml
• mugsy version 1.2.3
• The ape R package. To install, please follow the instructions under "All modules." Then, activate the environment (source activate PopCOGenT). Finally, run the Rscript install_ape.R from the Core genome sweep identification source directory.

Usage

Instructions for the usage of each module are provided in each module's source code directory.