Phylo3D-Trait
Interactive 3D visualization of continuous trait evolution on phylogenetic trees.
Phylo3D-Trait is a Python CLI/library for visualizing supplied continuous trait values and ancestral-state estimates across phylogenies. For dated trees, evolutionary depth can be displayed as time before present. The recommended renderer produces standalone WebGL2 HTML using fixed four-layer depth peeling for transparent curtain meshes.
What it accepts
- Newick or Nexus phylogenetic trees
- CSV/TSV node values for tips, internal nodes, and root
- continuous phenotypic, physiological, morphological, genomic, or other quantitative traits
What it produces
- interactive 3D rectangular phylograms
- continuous trait height/color mapping
- tip and ancestral-node inspection
- standalone offline-viewable HTML
- publication-oriented PNG and hybrid SVG export
What it does not do
Phylo3D-Trait does not infer phylogenies, date trees, fit evolutionary models, or perform ancestral-state reconstruction.
Start here
New user: Open the step-by-step Tutorial
The tutorial covers installation, input files, ancestral-node IDs, and the exact plotting command.
Quick start
pip install phylo3d-trait
python -m phylo3d_trait.cli template-values -t tree.nwk -o values_template.csv
python -m phylo3d_trait.cli plot \
-t tree.nwk \
-v values.csv \
-o tree3d.html \
--renderer four-layer \
--opacity 0.85
Install
- PyPI: https://pypi.org/project/phylo3d-trait/
- Zenodo DOI: https://doi.org/10.5281/zenodo.23044881