steve-federowicz/dendropy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

Introduction

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:

http://packages.python.org/DendroPy/

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.

If you have setuptools <http://pypi.python.org/pypi/setuptools>_ installed, you can install the latest public release of DendroPy directly from the Python Package Index <http://pypi.python.org/pypi/DendroPy/>_ by running::

sudo easy_install -U dendropy

Alternatively, if you have pip <http://pypi.python.org/pypi/pip>_ installed, you can run::

sudo pip install dendropy

If you download the source code archive from the Python Package Index <http://pypi.python.org/pypi/DendroPy/>_, you can unarchive it and install it from the local source by running::

tar -xvzf DendroPy-3.x.x.tar.gz
cd DendroPy-3.x.x
sudo python setup.py install

Documentation

A detailed example-rich "cookbook"-style tutorial on using DendroPy can be found here:

http://packages.python.org/DendroPy/tutorial/index.html

While the API reference can be found here:

http://packages.python.org/DendroPy/library/index.html

Source Code Repository

The DendroPy source code is version-controlled using Git <http://git-scm.com/>, and the DendroPy Git repository <http://github.com/jeetsukumaran/DendroPy> can be cloned by running::

git clone git://github.com/jeetsukumaran/DendroPy.git

Change History

The major changes (new features and bug fixes) in the development history of DendroPy can be found here:

http://packages.python.org/DendroPy/changes.html

More Information

More information, including tutorials, library API references, citation, license, etc. can be found on the DendroPy documentation website <http://packages.python.org/DendroPy/>_:

http://packages.python.org/DendroPy/