.. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy/DendroPy4/doc/source/_static/dendropy_logo.png
:align: right
:target: https://github.com/jeetsukumaran/DendroPy
:alt: DendroPy wordmark
+--------------------+-+---------------------+-+---------------------+-+-------------------+
| *automated tests:* | | *package version:* | | *documentation:* | | *test coverage:* |
| | | | | | | |
| |CI| | | |PyPI| | | |Docs| | | |Coverage| |
+--------------------+-+---------------------+-+---------------------+-+-------------------+
.. |CI| image:: https://github.com/jeetsukumaran/DendroPy/actions/workflows/ci.yaml/badge.svg
:target: https://github.com/jeetsukumaran/DendroPy/actions/workflows/ci.yaml
:alt: Continuous Integration build
.. |PyPI| image:: https://img.shields.io/pypi/v/DendroPy.svg
:target: https://pypi.org/project/DendroPy/
:alt: PyPI version
.. |Docs| image:: https://github.com/jeetsukumaran/DendroPy/actions/workflows/pages/pages-build-deployment/badge.svg
:target: https://jeetsukumaran.github.io/DendroPy/
:alt: Documentation Status
.. |Coverage| image:: https://codecov.io/gh/jeetsukumaran/DendroPy/graph/badge.svg?token=JwMfFOpBBD
:target: https://codecov.io/gh/jeetsukumaran/DendroPy
:alt: codecov coverage
.. |nbsp| unicode:: 0xA0
:trim:
-----
DendroPy is a Python library for phylogenetic computing.
It provides classes and functions for the simulation, processing, and
manipulation of phylogenetic trees and character matrices, and supports the
reading and writing of phylogenetic data in a range of formats, such as NEXUS,
NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some
useful phylogenetic operations, such as data conversion and tree posterior
distribution summarization, are also distributed and installed as part of the
libary. DendroPy can thus function as a stand-alone library for phylogenetics,
a component of more complex multi-library phyloinformatic pipelines, or as a
scripting "glue" that assembles and drives such pipelines.
The primary home page for DendroPy, with detailed tutorials and documentation, is at:
https://jeetsukumaran.github.io/DendroPy/
DendroPy is also hosted in the official Python repository:
http://pypi.org/project/DendroPy/
Requirements and Installation
=============================
The current version of DendroPy requires Python 3:
You can install DendroPy by running::
$ sudo pip install dendropy
More information is available here:
https://jeetsukumaran.github.io/DendroPy/downloading.html
Documentation
=============
Full documentation is available here:
https://jeetsukumaran.github.io/DendroPy/
This includes:
- `A comprehensive "getting started" primer <https://jeetsukumaran.github.io/DendroPy/primer/index.html>`_ .
- `API documentation <https://jeetsukumaran.github.io/DendroPy/library/index.html>`_ .
- `Descriptions of data formats supported for reading/writing <https://jeetsukumaran.github.io/DendroPy/schemas/index.html>`_ .
and more.
Citing
======
If you use any portion of DendroPy v5 in your research, please cite it as:
Moreno, M. A., Sukumaran, J., and M. T. Holder. 2024. DendroPy 5: a mature Python library for phylogenetic computing. arXiv preprint arXiv:2405.14120. https://doi.org/10.48550/arXiv.2405.14120
For BibTex users:
.. code-block:: bibtex
@misc{dendropy5,
title = {DendroPy 5: a mature Python library for phylogenetic computing},
author = {Moreno, Matthew Andres and Sukumaran, Jeet and Holder, Mark T.},
year = {2024},
keywords = {Populations and Evolution (q-bio.PE), FOS: Biological sciences, FOS: Biological sciences},
publisher = {arXiv},
doi = {10.48550/ARXIV.2405.14120},
url = {https://arxiv.org/abs/2405.14120},
copyright = {arXiv.org perpetual, non-exclusive license}
}
Earlier DendroPy versions can be cited as:
Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571. https://doi.org/10.1093/bioinformatics/btq228
Consider also leaving a `star on GitHub <https://github.com/jeetsukumaran/DendroPy/stargazers>`_!
License and Warranty
====================
Please see the file "LICENSE.rst" for details.
Developers
==========
- `Jeet Sukumaran <https://sukumaranlab.org/people/>`_
- `Mark Holder <https://phylo.bio.ku.edu/content/mark-t-holder>`_
- `Matthew Andres Moreno <https://mmore500.com/>`_
Raw data
{
"_id": null,
"home_page": "http://github.com/jeetsukumaran/DendroPy",
"name": "DendroPy",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": null,
"keywords": "phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics",
"author": "Jeet Sukumaran, Mark T. Holder, and Matthew Andres Moreno",
"author_email": "jeetsukumaran@gmail.com, mtholder@ku.edu, morenoma@umich.edu",
"download_url": "https://files.pythonhosted.org/packages/42/4b/6b300d145575ac7445e3b79b5c0c3a4ea441937278528b8dbd5b0aab42fc/DendroPy-5.0.1.tar.gz",
"platform": null,
"description": "\n.. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy/DendroPy4/doc/source/_static/dendropy_logo.png\n :align: right\n :target: https://github.com/jeetsukumaran/DendroPy\n :alt: DendroPy wordmark\n\n+--------------------+-+---------------------+-+---------------------+-+-------------------+\n| *automated tests:* | | *package version:* | | *documentation:* | | *test coverage:* |\n| | | | | | | |\n| |CI| | | |PyPI| | | |Docs| | | |Coverage| |\n+--------------------+-+---------------------+-+---------------------+-+-------------------+\n\n.. |CI| image:: https://github.com/jeetsukumaran/DendroPy/actions/workflows/ci.yaml/badge.svg\n :target: https://github.com/jeetsukumaran/DendroPy/actions/workflows/ci.yaml\n :alt: Continuous Integration build\n.. |PyPI| image:: https://img.shields.io/pypi/v/DendroPy.svg\n :target: https://pypi.org/project/DendroPy/\n :alt: PyPI version\n.. |Docs| image:: https://github.com/jeetsukumaran/DendroPy/actions/workflows/pages/pages-build-deployment/badge.svg\n :target: https://jeetsukumaran.github.io/DendroPy/\n :alt: Documentation Status\n.. |Coverage| image:: https://codecov.io/gh/jeetsukumaran/DendroPy/graph/badge.svg?token=JwMfFOpBBD\n :target: https://codecov.io/gh/jeetsukumaran/DendroPy\n :alt: codecov coverage\n.. |nbsp| unicode:: 0xA0\n :trim:\n\n\n-----\n\n\nDendroPy is a Python library for phylogenetic computing.\nIt provides classes and functions for the simulation, processing, and\nmanipulation of phylogenetic trees and character matrices, and supports the\nreading and writing of phylogenetic data in a range of formats, such as NEXUS,\nNEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some\nuseful phylogenetic operations, such as data conversion and tree posterior\ndistribution summarization, are also distributed and installed as part of the\nlibary. DendroPy can thus function as a stand-alone library for phylogenetics,\na component of more complex multi-library phyloinformatic pipelines, or as a\nscripting \"glue\" that assembles and drives such pipelines.\n\nThe primary home page for DendroPy, with detailed tutorials and documentation, is at:\n\n https://jeetsukumaran.github.io/DendroPy/\n\nDendroPy is also hosted in the official Python repository:\n\n http://pypi.org/project/DendroPy/\n\nRequirements and Installation\n=============================\n\nThe current version of DendroPy requires Python 3:\n\nYou can install DendroPy by running::\n\n $ sudo pip install dendropy\n\nMore information is available here:\n\n https://jeetsukumaran.github.io/DendroPy/downloading.html\n\nDocumentation\n=============\n\nFull documentation is available here:\n\n https://jeetsukumaran.github.io/DendroPy/\n\nThis includes:\n\n - `A comprehensive \"getting started\" primer <https://jeetsukumaran.github.io/DendroPy/primer/index.html>`_ .\n - `API documentation <https://jeetsukumaran.github.io/DendroPy/library/index.html>`_ .\n - `Descriptions of data formats supported for reading/writing <https://jeetsukumaran.github.io/DendroPy/schemas/index.html>`_ .\n\nand more.\n\nCiting\n======\n\nIf you use any portion of DendroPy v5 in your research, please cite it as:\n\n Moreno, M. A., Sukumaran, J., and M. T. Holder. 2024. DendroPy 5: a mature Python library for phylogenetic computing. arXiv preprint arXiv:2405.14120. https://doi.org/10.48550/arXiv.2405.14120\n\nFor BibTex users:\n\n.. code-block:: bibtex\n\n @misc{dendropy5,\n title = {DendroPy 5: a mature Python library for phylogenetic computing},\n author = {Moreno, Matthew Andres and Sukumaran, Jeet and Holder, Mark T.},\n year = {2024},\n keywords = {Populations and Evolution (q-bio.PE), FOS: Biological sciences, FOS: Biological sciences},\n publisher = {arXiv},\n doi = {10.48550/ARXIV.2405.14120},\n url = {https://arxiv.org/abs/2405.14120},\n copyright = {arXiv.org perpetual, non-exclusive license}\n }\n\nEarlier DendroPy versions can be cited as:\n\n Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571. https://doi.org/10.1093/bioinformatics/btq228\n\nConsider also leaving a `star on GitHub <https://github.com/jeetsukumaran/DendroPy/stargazers>`_!\n\nLicense and Warranty\n====================\n\nPlease see the file \"LICENSE.rst\" for details.\n\nDevelopers\n==========\n\n- `Jeet Sukumaran <https://sukumaranlab.org/people/>`_\n- `Mark Holder <https://phylo.bio.ku.edu/content/mark-t-holder>`_\n- `Matthew Andres Moreno <https://mmore500.com/>`_\n\n\n",
"bugtrack_url": null,
"license": "BSD",
"summary": "A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.",
"version": "5.0.1",
"project_urls": {
"Documentation": "https://jeetsukumaran.github.io/DendroPy/",
"Homepage": "http://github.com/jeetsukumaran/DendroPy",
"Source": "https://github.com/jeetsukumaran/DendroPy",
"Tracker": "https://github.com/jeetsukumaran/DendroPy/issues"
},
"split_keywords": [
"phylogenetics",
"phylogeny",
"phylogenies",
"phylogeography",
"evolution",
"evolutionary",
"biology",
"systematics",
"coalescent",
"population",
"genetics",
"phyloinformatics",
"bioinformatics"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "16967dcfffa89fc659669e697bcbdf01e7eac37ab0676aa242323a23366132a2",
"md5": "7e8c0f2824ad2ecad186918381dea3b5",
"sha256": "20066d300e65517119f885baf1061717bbb68cbb5190e611f3ff8b558e20cbc6"
},
"downloads": -1,
"filename": "DendroPy-5.0.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "7e8c0f2824ad2ecad186918381dea3b5",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.6",
"size": 459524,
"upload_time": "2024-06-02T07:40:13",
"upload_time_iso_8601": "2024-06-02T07:40:13.313065Z",
"url": "https://files.pythonhosted.org/packages/16/96/7dcfffa89fc659669e697bcbdf01e7eac37ab0676aa242323a23366132a2/DendroPy-5.0.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "424b6b300d145575ac7445e3b79b5c0c3a4ea441937278528b8dbd5b0aab42fc",
"md5": "072f0650e78de803122ec9d77f0ac826",
"sha256": "f2815e7649a6fe2924ff3fdf00a660c948dc6f3316e303b8b022f74cc75ca42e"
},
"downloads": -1,
"filename": "DendroPy-5.0.1.tar.gz",
"has_sig": false,
"md5_digest": "072f0650e78de803122ec9d77f0ac826",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 395057,
"upload_time": "2024-06-02T07:40:15",
"upload_time_iso_8601": "2024-06-02T07:40:15.719994Z",
"url": "https://files.pythonhosted.org/packages/42/4b/6b300d145575ac7445e3b79b5c0c3a4ea441937278528b8dbd5b0aab42fc/DendroPy-5.0.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-06-02 07:40:15",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "jeetsukumaran",
"github_project": "DendroPy",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "dendropy"
}
JSON
