aphylogeo 0.3.2

A phylogenetic and geographic analysis tool



aPhyloGeo

🌳 Multi-platform application for analyze 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.

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

1️⃣ 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

2️⃣ 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

⚒️ Installation

Linux UNIX, Mac OS & Windows versions

aPhyloGeo is available as a Python script.

Prerequisites

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.

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

poetry install

Usage

Poetry will handle the virtual environment automatically. if you want to use the virtual environment manually, you can use the following command:

poetry shell

⚠️ 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.

• Bootstrap threshold: Number of replicates threshold to be generated for each sub-MSA (each position of the sliding window)
• Window length: Size of the sliding window
• Step: Sliding window advancement step
• Distance choice: distance selection
  • '1' for Least Square (LS) distance (version 1.0)
  • '2' for Robinson and Foulds (RF) distance
  • '3' for Euclidean distance
• Distance threshold: LS distance threshold at which the results are most significant
• Alignment method: algorithm selection for sequence alignment
  • '1' for pairwise2
  • '2' for MUSCLE
  • '3' for CLUSTALW
  • '4' for MAFFT
• Fit method: gap selection elongation
  • '1' for Wider Fit by elongating with Gap (starAlignment)
  • '2' for Narrow-fit prevent elongation with gap when possible

✔️ References

1️⃣ Calculation of distance between phylogenetic tree: Least Square metric

• Cavalli-Sforza, L. L., & Edwards, A. W. (1967). Phylogenetic analysis. Models and estimation procedures. American journal of human genetics, 19(3 Pt 1), 233.
• Felsenstein, J. (1997). An alternating least squares approach to inferring phylogenies from pairwise distances. Systematic biology, 46(1), 101-111.
• Makarenkov, V., & Lapointe, F. J. (2004). A weighted least-squares approach for inferring phylogenies from incomplete distance matrices. Bioinformatics, 20(13), 2113-2121.

2️⃣ Calculation of distance between phylogenetic tree: Robinson-Foulds metric

• Robinson, D.F. and Foulds, L.R., 1981. Comparison of phylogenetic trees. Mathematical biosciences, 53(1-2), pp.131-147.

3️⃣ Dataset full description: Analysis of genetic and climatic data of SARS-CoV-2

• Koshkarov, A., Li, W., Luu, M. L., & Tahiri, N. (2022). Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2.
• Li, W., & Tahiri, N. (2023). aPhyloGeo-Covid: A Web Interface for Reproducible Phylogeographic Analysis of SARS-CoV-2 Variation using Neo4j and Snakemake.

📧 Contact

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