Comparative Study of HGT Inference Methods

Code to reproduce the results of the paper, "Horizontal Gene Transfer Inference: Gene presence-absence outperforms gene trees" where we perform a comparative study of HGT inference methods. See: preprint in bioRxiv.

The project is organized into three main steps (01, 02, 03), each containing sequentially numbered Jupyter notebooks. Supporting scripts and helper functions referenced in these notebooks are located in the src/ and lib/ directories.

Notebook Usage

• Execute notebooks cell by cell instead of using 'Run All'.
• Many cells contain markdown instructions for running external shell programs. This is because several processes are computationally intensive and intended for HPC environments with multiprocessing capabilities.

Data Management

• The data directory is initially empty in this repository.
• Running the notebooks sequentially will populate the data directory with:
  • Downloaded files
  • Processed results
  • Generated figures
• Alternatively, a complete dataset including results and figures can be downloaded from the Zenodo link in the paper.

Required python packages

A Mamba/Conda environment called hgt_analyses was used for all the analyses. This environment with all required packages can easily be created again using the mamba_packages.yml file, using the following command:

mamba env create -f mamba_packages.yml

If you use Conda instead of Mamba just replace mamba with conda in the above command.