GenALLYgn - Genes alignment and visualisation tool

By Ally Champoux, Université de Sherbrooke, 24/09/2026

This repository contains scripts used to align and visualise small DNA fragments such as phage genomes.

Installation

You first have to clone this repository

git clone https://github.com/allychamp/Phage_alignement_visualisation.git

It contains the following tree:

├── Image
├── LICENSE
├── README.md
├── config.yaml
└── src
    ├── __init__.py
    ├── blast_links.py
    ├── main.py
    ├── parser.py
    └── plotter.py

Note that you should have conda or miniconda installed to run this pipeline.

The dependencies can be installed with the yaml file in this repo. This will create a conda environment containing all the dependencies. To do so, run this command:

conda env create -f genALLYgn_env.yml

Usage

The tool takes in input a combination of a genbank file and a protein fasta file per sample (one folder per file type) Before launching the script, first complete the config file:

Variable in config file	Description
genomes_dir	Path to a folder containing all GenBank files
faa_dir	Path to a folder containing all protein FASTA files
all_proteins	Path to the directory where the merged multi-FASTA protein file should be saved
blast_file	Path (including filename) to the directory where the all-vs-all BLAST results file should be saved
cds_table	Path to the summary CSV of all CDS predictions (used for color-coding functions in the visualization)
color_table	Path to the CSV mapping each function to its desired color (used for color-coding functions in the visualization)
output_svg	Path (including file extension) for the desired output file
blast.identity_threshold	Minimum percent identity required between query and subject proteins for a link to be kept (e.g. 30 = at least 30% identity)
blast.coverage_threshold	Minimum percent of the query protein length that must align with the subject for a link to be kept (e.g. 60 = at least 60% coverage)
blast.num_threads	Number of threads to use for the BLAST analysis; more threads speeds up the run
plot.spacing	Spacing between genomes in the plot
plot.label_width	Width of the genome labels in the plot
plot.genome_order	Order in which genomes should appear (must match the genome file names); if not specified, genomes will be ordered by similarity

Once all the paths are set up, activate your conda environment:

conda activate genALLYgn_env

Then, go to the directory containing the scripts and run the following command:

python -m src.main

Citation

Please keep an eye out for the preprint of this tool. In the meantime, please cite this repository if you use it in your work: Champoux, A., Jacques, P., & Fortier, L. (2026). GeneALLYgn [Computer software]. https://github.com/allychamp/phage-genome-analysis-pipeline