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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.
aPhyloGeo is available as a Python package.
aPhyloGeo can be installed directly from the Python Packaging Index,
python3 -m pip install aPhyloGeoThis package use Poetry dependency management and packaging tool for Python. Poetry installation guide can be found here: Poetry Install.
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
Poetry automatically manages the virtual environment. If manual activation is preferred, the following command can be used
poetry shell
Launch the application and tutorial example using the following command:
make
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.
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).
We offer several comprehensive tutorials to help users get started with the package.
You can also refer to the documentation for more details. Some useful links:
💡 If you are using our algorithm in your research, please cite our recent papers:
1️⃣ Li, W. & Tahiri, N. (2024). Host-Virus Cophylogeny Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts. Preprint researchsquare
2️⃣ 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
3️⃣ 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
Please email us at: Nadia.Tahiri@USherbrooke.ca for any questions or feedback.