ete3
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
4 of 63 committers (6.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
Basic Info
- Host: GitHub
- Owner: etetoolkit
- License: gpl-3.0
- Language: Python
- Default Branch: ete4
- Homepage: http://etetoolkit.org
- Size: 127 MB
Statistics
- Stars: 843
- Watchers: 34
- Forks: 222
- Open Issues: 243
- Releases: 10
Topics
Metadata Files
README.md
Overview
ETE (Environment for Tree Exploration) is a toolkit that assists in the automated manipulation, analysis and visualization of trees. It is mainly written in Python, and includes many extra functionalities for phylogenetic trees.
Its main features include:
- Read and write support for trees in Newick and Nexus formats
- Multiple functions for traversing, searching and manipulating tree topologies and node annotations
- Integration with NCBI Taxonomic database
- Integration with GTDB database
- Programmatic visualization framework
- Visualization of huge trees based on adaptive zooming
- Comparing trees
- Phylogenetic functions
- orthology detection
- phylogenetic distance
//: # (TODO: We used to claim these too, but they should be checked and possibly fixed: Command line tools phylogenetic reconstruction protocols tree comparison tree diff )
//: # (TODO: Remove, or put back this link once the website is updated: The official website of ETE is http://etetoolkit.org. You can find downloading instructions and further documentation there. )
If you use ETE, please cite:
Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi:
10.1093/molbev/msw046
Installation
Quick way
sh
pip install ete4
will get you the latest release from PyPI.
... or with conda
sh
conda install conda-forge::ete4
to get it from conda-forge.
... or using the very latest from the repository
sh
pip install --force-reinstall https://github.com/etetoolkit/ete/archive/ete4.zip
if you want to be up-to-date with the very last commit done, even before release.
For local development
To install ETE in a local directory to help with the development, you can:
- Clone this repository (
git clone https://github.com/etetoolkit/ete.git) - Install dependecies
- If you are using conda:
conda install -c conda-forge cython bottle cheroot brotli numpy scipy - Otherwise, you can install them with
pip install <dependencies>
- If you are using conda:
- Build and install ete4 from the repository's root directory:
pip install -e .
Optional dependencies
If you want to use the treeview module (which depends on
PyQt), you can
add [treeview] to the pip installation.
For example with pip install -e .[treeview] for a local editable
installation. Or pip install -e .[treeview,test,doc,render_sm] to
also include the modules for testing, generating the documentation,
and smartview file rendering.
Exploring a tree
To simply load a tree from a file (my_tree.nw) and start exploring
it interactively, you can use the ete4 utility and run:
sh
ete4 explore -t my_tree.nw
Or start a python session and write:
```py from ete4 import Tree
t = Tree(open('my_tree.nw'))
t.explore() ```
It will open a browser window with an interface to explore the tree.
Documentation
Most documentation is automatically generated with
sphinx from the contents of the doc
directory, and is available at https://etetoolkit.github.io/ete/ .
Gallery of examples
There is also an ETE Gallery with a tutorial, examples and course material to learn about the graphical capabilities of ETE.
Getting support
Rather than sending direct support-related emails to the developers, it is better to keep the communication public.
For question on how to use ETE in the bioinformatics context, use
Biostars with the etetoolkit tag, or stack
overflow.
For bug reports, feature requests and general discussion, use https://github.com/etetoolkit/ete/issues
For more technical problems, you can also use the official ETE mailing list at https://groups.google.com/d/forum/etetoolkit. To avoid spam, messages from new users are moderated. Expect some delay until your first message appears after your account is validated.
For any other inquiries (collaborations, sponsoring, etc), please contact jhcepas@gmail.com.
Tests
You can launch some tests by running:
sh
./run_tests.py
Contributing and bug reporting
https://github.com/etetoolkit/ete/wiki/Contributing
Roadmap
https://github.com/etetoolkit/ete/wiki/ROADMAP
Owner
- Name: ETE Toolkit
- Login: etetoolkit
- Kind: organization
- Email: jhcepas@gmail.com
- Website: http://etetoolkit.org
- Repositories: 13
- Profile: https://github.com/etetoolkit
A Python framework for the analysis and visualization of trees.
GitHub Events
Total
- Create event: 10
- Release event: 3
- Issues event: 24
- Watch event: 53
- Issue comment event: 43
- Push event: 163
- Gollum event: 2
- Pull request event: 18
- Fork event: 13
Last Year
- Create event: 10
- Release event: 3
- Issues event: 24
- Watch event: 53
- Issue comment event: 43
- Push event: 163
- Gollum event: 2
- Pull request event: 18
- Fork event: 13
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jaime Huerta-Cepas | j****s@g****m | 1,750 |
| Jordi | j****l@g****m | 1,007 |
| jorgebotas | j****t@p****m | 496 |
| garamonfok | s****s@g****m | 221 |
| dengzq1234 | d****4@g****m | 133 |
| garamonfok | f****s@b****g | 101 |
| DiegoBernabeLopez | d****z@g****m | 65 |
| Renato Alves | a****c@g****m | 26 |
| Alisha Mechtley | a****n@m****u | 17 |
| Finlay Maguire | f****e@g****m | 14 |
| Ivan | i****n@i****) | 10 |
| scapella | s****u@g****m | 10 |
| DiegoBernabeLopez | d****z@s****l | 9 |
| garamonfok | f****o@e****) | 9 |
| jaime | j****e@l****) | 5 |
| francisco | f****o@g****) | 4 |
| fransua | f****s@b****n | 4 |
| jhuerta | j****a@t****) | 4 |
| Dillon Barker | d****r@g****m | 4 |
| Christopher Chavez | c****z@g****s | 3 |
| JohnBioinf | j****n@b****e | 3 |
| Sam Manzi | m****m@g****m | 3 |
| francois | f****o@g****) | 3 |
| jhuerta | j****a@c****s | 3 |
| Renato Alves | r****s@i****t | 3 |
| jhuerta | j****a@v****) | 2 |
| Kartik Raj | k****r@i****n | 2 |
| Erick Matsen | e****n@g****m | 2 |
| Daniel Burkhardt | b****b@g****m | 2 |
| Alan | a****7@u****m | 2 |
| and 33 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 101
- Total pull requests: 122
- Average time to close issues: 7 months
- Average time to close pull requests: 8 months
- Total issue authors: 75
- Total pull request authors: 42
- Average comments per issue: 2.14
- Average comments per pull request: 0.97
- Merged pull requests: 82
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 23
- Pull requests: 19
- Average time to close issues: 3 days
- Average time to close pull requests: 25 days
- Issue authors: 20
- Pull request authors: 7
- Average comments per issue: 0.13
- Average comments per pull request: 0.79
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dengzq1234 (17)
- lab83bio (2)
- tommyfuu (2)
- sirno (2)
- metehaansever (2)
- lenacoll (2)
- lm-jkominek (2)
- Gullumluvl (2)
- harryrichman (2)
- pathogen-detection (2)
- cmayer (2)
- maremita (1)
- Anthony-J-G (1)
- zhaofeng-shu33 (1)
- danrans123 (1)
Pull Request Authors
- dengzq1234 (26)
- jorgebotas (26)
- jordibc (16)
- jhcepas (7)
- mmore500 (2)
- sirno (2)
- hjgwak (2)
- mwittep (2)
- ArnaudBelcour (2)
- nsoranzo (2)
- cfblaeb (2)
- emollier (2)
- terrycojones (2)
- maclandrol (1)
- bilalix (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 95,000 last-month
- Total docker downloads: 50,692
-
Total dependent packages: 94
(may contain duplicates) -
Total dependent repositories: 342
(may contain duplicates) - Total versions: 32
- Total maintainers: 1
pypi.org: ete3
A Python Environment for (phylogenetic) Tree Exploration
- Homepage: http://etetoolkit.org
- Documentation: http://etetoolkit.org/docs/latest/tutorial/index.html
- License: GPLv3
-
Latest release: 3.1.3
published almost 3 years ago
Rankings
Maintainers (1)
conda-forge.org: ete3
- Homepage: http://etetoolkit.org
- License: GPL-3.0-only
-
Latest release: 3.1.2
published over 5 years ago
Rankings
Dependencies
- bottle *
- brotli *
- numpy *
- pyqt5 *
- actions/checkout v2 composite
- actions/setup-python v4 composite
- peaceiris/actions-gh-pages v3 composite