aphylogeo 2.0.0

A phylogenetic and geographic analysis tool



aPhyloGeo

🌳 Multi-platform application for analyzing phylogenetic trees with climatic parameters

Table of Contents

1. About the project
2. Installation
   • Linux/UNIX, Mac OS and Windows versions
3. Settings
4. References
5. Contact

📝 About the project

aPhyloGeo is a powerful and versatile bioinformatics pipeline specifically designed for the analysis of phylogeography. Developed by the dedicated team led by Professor Nadia Tahiri at the University of Sherbrooke in Quebec, Canada, this open-source multi-platform application is implemented in Python. It serves as a valuable tool for researchers and scientists interested in unraveling the intricate relationships between genetic sequences and geographic locations.

Reference: Chenoweth Galaz, Ana Laura, and Nadia Tahiri. "aPhyloGeo: a Python application for correlating genetic and climatic conditions." Bioinformatics 41.11 (2025): btaf574.

⚒️ Installation

Linux UNIX & Windows versions

aPhyloGeo is available as a Python package.

Installation from PyPI via pip

aPhyloGeo can be installed directly from the Python Packaging Index,

python3 -m pip install aPhyloGeo

Installation from Source via Poetry

This package use Poetry dependency management and packaging tool for Python. Poetry installation guide can be found here: Poetry Install. ⚠️ For windows installation it's recommended to launch powershell in Administrator mode.

Installation of Poetry is using the following commands:

pip install poetry

Once Poetry is installed, you can clone the repository and install the package using the following commands:

poetry install

Usage

Poetry automatically manages the virtual environment. If manual activation is preferred, the following command can be used

poetry shell

Run the application

Launch the application and tutorial example using the following command:

make

⚠️ Assuming Python 3.8 or higher is installed on the machine, these scripts should run well with the libraries installed.

You can also launch the package using the make command from your terminal when you are in the root. This command will use the Makefile to run the script. If you use the command make clean, it will erase the output.csv file previously created with the first command.

🚀 Settings

The aPhyloGeo software can be encapsulated in other applications and applied to other data by providing a YAML file. This file will include a set of parameters for easy handling (see Wiki documentation).

📚 Tutorials

We offer several comprehensive tutorials to help users get started with the package.

📖 Documentation

You can also refer to the documentation for more details. Some useful links:

• Installation guide
• Tutorial
• Worflow
• Contribution guidelines
• aPhyloGeo wiki
• aPhyloGeo Sphinx
• zenodo - DOI:17290768

✔️ References

💡 If you are using our algorithm in your research, please cite our recent papers:

1️⃣ Chenoweth Galaz, A. L., & Tahiri, N. (2025). aPhyloGeo: a Python application for correlating genetic and climatic conditions. Bioinformatics, 41(11), btaf574

2️⃣ Li, W. & Tahiri, N. (2024). Host-Virus Cophylogeny Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts. Viruses, 16(7), p.1133

3️⃣ Gagnon, J. & Tahiri, N. (2024). Ecological and Spatial Influences on the Genetics of Cumacea (Crustacea: Peracarida) in the Northern North Atlantic. Proceeding in SciPy 2024, Tacoma, WA, USA

4️⃣ Li, W. & Tahiri, N. (2023). aPhyloGeo-Covid: A Web Interface for Reproducible Phylogeographic Analysis of SARS-CoV-2 Variation using Neo4j and Snakemake. Proceeding in SciPy 2023, Auxtin, TX, USA

5️⃣ Koshkarov, A., Li, W., Luu, M. L., & Tahiri, N. (2022). Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2. Proceeding in SciPy 2022, Auxtin, TX, USA

📧 Contact

Please email us at: [e-mail] for any questions or feedback.