CFE Tree Maker

CFE Tree Maker is a Python script that allows you to create and visualize phylogenetic trees in a simple and automated way.

Features

• Produces phylogenetic trees in PDF format.
• Customizable label colors and styles.
• Supports Python 3.10 and higher.

Installation

uv tool install cfetree

Usage

Note: CFE Tree Maker requires trees be generated from Clustal!

To use CFE Tree Maker, run the following command:

cfetree input.newick output.pdf

Alternatively, import it into your own project:

from cfetree import load_tree, export_tree

t = load_tree("A,B,C;")
export_tree(t, "/tmp/tree.pdf", "My tree")

This will generate a PDF file containing the phylogenetic tree.

Contributing

Contributions to CFE Tree Maker are welcome! If you find any issues or have suggestions for improvements, please open an issue or submit a pull request on the GitHub repository.

Development

Use uv to manage the environment.

Install all dev dependencies:

uv sync --extra test --extra dev

Test:

uv run pytest

Lint:

uv run ruff check

Format:

uv run ruff format

Type-check:

uv run mypy cfetree tests

License

CFE Tree Maker is licensed under the GNU General Public License v3.0. See the LICENSE file for more details.