DendroPy Phylogenetic Computing Library

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.

Prerequisites

DendroPy is a pure-Python library with no dependencies, and 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.

Changed in version 3.2.0: Python 2.4 support added.

Installing

DendroPy is fully easy-installable and can be installed using pip:

$ sudo pip install dendropy

or setuptools:

$ sudo easy_install -U dendropy

if these are available on your system.

These, and other ways of obtaining and installing DendroPy (e.g., by downloading the DendroPy source code archive, or by cloning the DendroPy Git repository), are discussed in detail in the “Downloading and Installing DendroPy” section.

Documentation

Downloading and Installing DendroPy

The many ways to get DendroPy up and running on your system.

DendroPy Tutorial

A detailed tutorial on how to use the DendroPy library, with lots of annotated practical examples and code walk-throughs.

DendroPy Library API Reference

The technical details of the modules, classes and methods of the DendroPy library. Almost all of this information is also readily available from the Python interpreter by invoking help() on an object or name.

SumTrees User Manual

How to use SumTrees, an application script bundled with DendroPy that faciliates the summarization of non-parameteric bootstrap or Bayesian posterior probability support for splits or clades on phylogenetic trees.

Change History

A summary of major changes (new features, bug fixes, bug creations, etc.) of each release of DendroPy.

Citation

If you use this library either in whole or in part in your analysis, or use any code derived from it, please cite it as (replacing the version numbers with ones corresponding to the version that you used):

Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics 26: 1569-1571.

Suggestions, Comments, Help, or Bug Reports

The DendroPy Users discussion group is available for general discussion on the usage of the DendroPy library. If you want more information on how to use a particular feature or carry out specific task, would like to request a new feature or change an existing one, or even just want to make some general comments on the DendroPy library, you should post a message to the DendroPy Users discussion group. I follow and respond to messages on this group fairly regularly, so you should get a response within 24 hours. If you prefer, you can also contact me directly via e-mail at jeet@ku.edu, but by posting to the DendroPy Users group forum, you allow other users, current as well as future, to benefit from the discussion and results.

The DendroPy Users discussion group is also a suitable forum for the reporting of bugs or errors encountered with DendroPy, as most other users would also appreciate learning of problems and issues with library. However, again, if you prefer you can contact me directly via e-mail at jeet@ku.edu.

Copyright, License and Warranty

The DendroPy library and the DendroPy logo are:

Copyright 2009-2010 Jeet Sukumaran and Mark T. Holder

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
• The names of its contributors may not be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL JEET SUKUMARAN OR MARK T. HOLDER BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Acknowledgments

Portions of DendroPy were developed under CIPRES, a multi-site collaboration funded by the NSF Information Technology Research (ITR) program grant entitled “BUILDING THE TREE OF LIFE: A National Resource for Phyloinformatics and Computational Phylogenetics” and NSF ATOL grant 0732920 to Mark Holder.