ete3

What it is and what it does

ETE3 is a mature Python toolkit for phylogenetic tree work, supporting reconstruction, manipulation, analysis, and visualization of tree-structured data. It is primarily designed for researchers in phylogenetics and genomics, though it can handle any tree-like data structure. The package has been actively maintained since its first release in 2015 and is currently at version 3.1.3, with a repository showing recent activity and a moderate user base.

The toolkit provides both programmatic APIs for tree operations and visualization capabilities, including support for Qt-based graphical output. Installation carries high friction, indicating the presence of compiled dependencies or system-level requirements that may need manual setup. The codebase is mature and stable, and the package is widely used in the bioinformatics community, though users should be aware of the GPLv3 copyleft licensing constraint.

Use it for:

• Reconstruct and manipulate phylogenetic trees from sequence alignment or distance data in genomics research.
• Visualize and compare evolutionary relationships between organisms or genes in publication-quality formats.
• Analyze tree topology, branch lengths, and clustering patterns programmatically in bioinformatics pipelines.
• Convert between tree file formats (Newick, NHX, etc.) and perform tree-to-tree comparisons.
• Build custom tree-based analyses by scripting tree traversal and node manipulation in Python.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

ETE3 reconstructs, manipulates, analyzes, and visualizes phylogenetic trees and other tree-like data structures through a Python API.

Yes, if you work in phylogenetics or genomics and need tree manipulation and visualization. The package is mature, actively maintained, and well-established in its domain. However, be prepared for high installation friction (likely system dependencies), verify Python version compatibility before installing, and ensure GPLv3 licensing aligns with your project's constraints.

Install

ete3 on PyPI

pip install ete3

uv add ete3

poetry add ete3

Installing ete3

Before you install

Installation friction is high; the package ships as a source tarball and has no declared runtime dependencies, suggesting compiled components or system-level prerequisites may be required during build.

License in practice

GPLv3 copyleft license means any derivative work or distribution must also be open-source under compatible terms; suitable for research and open-source projects but requires careful review before use in proprietary software.

Quickstart

pip install ete3
from ete3 import Tree
t = Tree('(A:1,B:1)C;')
print(t)

High install friction suggests system libraries or build tools may be required; Qt support may require additional X11 or graphical environment setup on some systems.

Verify before relying

• What system libraries or compiled dependencies are needed at build time (the high friction suggests non-trivial prerequisites).
• Whether Qt support (listed in classifiers) is optional or required, and what additional setup it demands.
• Current Python version compatibility (requires_python is unspecified in the metadata).

Package facts

Evidence: ete3-3.1.3.tar.gz

Keywords: tree, tree reconstruction, tree visualization, tree comparison, phylogeny, phylogenetics, phylogenomics

Tags

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