ete3
A Python Environment for (phylogenetic) Tree Exploration
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- 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.
- 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 · maintenance · safety
GPLv3 (copyleft) — 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.
last release 2023-05-02 (1200 days) · last repo commit 2026-06-01 · 885 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 100,419 downloads/mo, #12,985 on PyPI
Alternatives
Verify before relying
pip install ete3
from ete3 import Tree
t = Tree('(A:1,B:1)C;')
print(t)- 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).
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 on it.
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
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.
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.
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)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
| License | GPLv3 copyleft |
| Python support | Not specified |
| Install friction | High. Source build required |
| Runtime dependencies | None |
| Maintenance | Actively maintained 1,200 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 100,419 / month, #12,985 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 6 - MatureEnvironment :: ConsoleEnvironment :: X11 Applications :: QtIntended Audience :: DevelopersIntended Audience :: Other AudienceIntended Audience :: Science/ResearchLicense :: OSI Approved :: GNU General Public License (GPL)Natural Language :: EnglishOperating System :: MacOSOperating System :: Microsoft :: WindowsOperating System :: POSIX :: LinuxProgramming Language :: PythonTopic :: Scientific/Engineering :: Bio-InformaticsTopic :: Scientific/Engineering :: VisualizationTopic :: Software Development :: Libraries :: Python Modules |
Evidence: ete3-3.1.3.tar.gz
Tags
Let your AI agent find packages like this
Example. Real query, live index.
You found this page by searching. An agent finds it by wishing: SkillFed indexes 14,416 PyPI packages by what they can do, searchable in plain language.
wish › “phylogenetic tree visualization”
- ete3ETE3 reconstructs, manipulates, analyzes, and visualizes phylogenetic…
- biopythonBiopython provides Python tools for computational molecular biology,…
- scikit-bioscikit-bio provides data structures, algorithms, and educational…
Give your agent the search over MCP, or paste the wish link into any chat.
More Python Modules packages
Converts domain names between Unicode and ASCII-compatible encoding (Punycode) according to IDNA 2008 and Unicode Technical Standard 46, with security validation and broader script coverage than the standard library.
Install it if you work with internationalized domain names, need to validate domains, or use HTTP clients that depend on it transitively.
Setuptools is a Python build backend and package management tool that handles building, distributing, and installing Python packages, including support for C/C++ extension modules.
PyYAML parses and emits YAML 1.1 data format, enabling serialization and deserialization of configuration files and Python objects to and from human-readable YAML text.
Pydantic validates Python data structures against type hints, coercing and checking input at runtime to ensure it matches a declared schema.
Provides reusable metadata objects for use with PEP-593 `typing.Annotated` to express common constraints like bounds, collection sizes, and predicates on types.
Install it if you use or build libraries that need to express type constraints in a standardized, inspectable way—or if you want to annotate your own types with…
Provides runtime tools to inspect and introspect Python type annotations, enabling programmatic examination of type hints at execution time.
See also biopython · dtreeviz · ai-edge-model-explorer · nutree · pyranges · scikit-bio · py_trees · anytree · open3d · asciitree