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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 Packaging Index (PyPI):

http://pypi.org/project/DendroPy/

Requirements and Installation

The current version of DendroPy requires Python 3.

You can install DendroPy by running::

$ python -m pip install dendropy

For Conda users, DendroPy can be installed from the conda-forge channel:

$ conda install -c conda-forge 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:

and more.

Citing

If you use any portion of DendroPy v5 in your research, please cite it as:

Moreno, M. A., Holder, M. T., & Sukumaran, J. (2024). DendroPy 5: a mature Python library for phylogenetic computing. Journal of Open Source Software, 9(101), 6943, https://doi.org/10.21105/joss.06943

For BibTex users:

@misc{dendropy5,
  doi = {10.21105/joss.06943},
  url = {https://doi.org/10.21105/joss.06943},
  year = {2024},
  publisher = {The Open Journal},
  volume = {9},
  number = {101},
  pages = {6943},
  author = {Matthew Andres Moreno and Mark T. Holder and Jeet Sukumaran},
  title = {DendroPy 5: a mature Python library for phylogenetic computing},
  journal = {Journal of Open Source Software}
}

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!

License and Warranty

Please see the file "LICENSE.rst" for details.

Developers

Metadata

Release files for DendroPy 5.1.3

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Source distribution (sdist)

Source distribution for DendroPy 5.1.3
File	Size	Uploaded	Provenance
dendropy-5.1.3.tar.gz	433.2 kB	Oct 23, 2026	Without provenance	Details

Built distribution (wheel)

Table of built distributions (wheels) for DendroPy 5.1.3
File	Interpreter	ABI	Platform	Reset
dendropy-5.1.3-py3-none-any.whl 506.6 kB Oct 23, 2026 Without provenance	Python 3	none	any	Details

Total release size: 939.8 kB

Release files / dendropy-5.1.3.tar.gz

Download URL	dendropy-5.1.3.tar.gz
Size	433.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`eb2d622b8900e08e4810a08a925163458898ea870f04f0db68b6f04316645f73`
BLAKE2b-256 checksum How to use checksums	`aa4843147b629856479e493ea4d51be0221ee9212c8fe4a7b344041715115f62`
Upload date	Oct 23, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.13.16`

Release files / dendropy-5.1.3-py3-none-any.whl

Download URL	dendropy-5.1.3-py3-none-any.whl
Size	506.6 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`2117e7ff5821f879184051f3e278ee229b420a215b0dabb0c6af72540d9d3186`
BLAKE2b-256 checksum How to use checksums	`34d7238ae3126686e9b16baed14d8d2da29cea91e7fb59ae1780622a88396bd1`
Upload date	Oct 23, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.13.16`

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