A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
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:
Requirements and Installation
DendroPy runs under any version of Python 2 from 2.4 upwards (i.e., Python 2.4, 2.5, 2.6, 2.7, etc.). At present, it does not run under Python 3.
$ sudo easy_install -U dendropy
Alternatively, if you have pip installed, you can run:
$ sudo pip install dendropy
$ tar -xvzf DendroPy-3.12.0.tar.gz $ cd DendroPy-3.12.0 $ sudo python setup.py install
A detailed example-rich “cookbook”-style tutorial on using DendroPy can be found here:
While the API reference can be found here:
Source Code Repository
$ git clone git://github.com/jeetsukumaran/DendroPy.git
The major changes (new features and bug fixes) in the development history of DendroPy can be found here:
More information, including tutorials, library API references, citation, license, etc. can be found on the DendroPy documentation website:
The current release of DendroPy is version 3.12.0 (revision: 91b552d, None).