🗺️ PhyloGeoPlot

Table of Contents About the project Installation Dependencies Basic usage Documentation Examples Tests License Citation

A Python toolkit for phylogeographic visualization linking phylogenetic and geographic data

📝 About the project

PhyloGeoPlot is a powerful Python package for linked visualization of phylogenetic trees and geographic occurrence data. It connects taxa represented in a phylogenetic tree to their geographic coo[...]

Key goals:

• simplify phylogeographic figure production;
• support publication-quality visual outputs;
• provide reproducible pipelines for biogeographic analyses.

⚙️ Installation

Install from PyPI:

pip install phylogeoplot

PhyloGeoPlot requires Python >= 3.10.

📦 Dependencies

Main dependencies are installed automatically with pip:

• Biopython
• Cartopy
• Rasterio
• Matplotlib
• Pandas
• NumPy
• scikit-image

💻 Basic usage

from phylogeoplot.visualisation.tree_to_map_raster import PhyloGeoPlotter

plotter = PhyloGeoPlotter(
    nwk_file="sequences_tree.nwk",
    gps_file="coordinates.csv",
    offset_file="offsets.csv",
    raster_file="environment.tif",
    raster_band=1,
)

plotter.plot()
plotter.save(output_dir="output")

Raster input is optional.

📖 Documentation

Detailed documentation is available in the PhyloGeoPlot Wiki.

Useful pages:

• Installation
• Input Data
• Preprocessing
• Visualization
• Examples
• Testing and Development
• Troubleshooting
• Citation

📚 Examples

The repository contains sample datasets and walkthrough notebooks for:

• Malagasy Coffea
• North Atlantic Cumacea

See the Examples page for details.

✅ Tests

Run the test suite with:

python -m pytest -v

📋 License

PhyloGeoPlot is distributed under the MIT License.

✏️ Citation

Citation information will be added here following publication.

📧 Contact

Please email us at: Nadia.Tahiri@USherbrooke.ca for any questions or feedback.