colorclade 0.3.0

colorclade draws phylogenies with hierarchical coloring for easier visual comparison.

colorclade draws phylogenies with hierarchical coloring for easier visual comparison

• Free software: MIT license
• Repository: https://github.com/mmore500/colorclade
• Documentation: https://github.com/mmore500/colorclade/blob/master/README.md

Install

python3 -m pip install colorclade

Example Usage

from colorclade import draw_colorclade_tree

fig, axes = plt.subplots(1, 2)
draw_colorclade_tree(
    alifestd_df1,
    taxon_name_key="taxon",
    ax=axes.flat[0],
    backend="biopython",
)
draw_colorclade_tree(
    alifestd_df2,
    taxon_name_key="taxon",
    ax=axes.flat[1],
    backend="biopython",
    label_tips=False,
)
axes.flat[1].set_xlim(reversed(axes.flat[1].get_xlim()))
fig.set_size_inches(7, 2.5)
plt.tight_layout()

See tests/test_draw_colorclade_tree.py for full example code.

Citing

If colorclade contributes to a scientific publication, please cite it as

Matthew Andres Moreno. (2024). mmore500/colorclade. Zenodo. https://doi.org/10.5281/zenodo.10802404

@software{moreno2024colorclade,
  author = {Matthew Andres Moreno},
  title = {mmore500/colorclade},
  month = mar,
  year = 2024,
  publisher = {Zenodo},
  doi = {10.5281/zenodo.10802404},
  url = {https://zenodo.org/doi/10.5281/zenodo.10802404}
}

Consider also citing Biopython and matplotlib. And don't forget to leave a star on GitHub!