DendroPy
Phylogenetic Computing Library
DendroPy is a Python library for phylogenetic scripting, simulation, data processing and manipulation by Jeet Sukumaran and Mark T. Holder. DendroPy provides classes and functions for working with phylogenetic data such as trees and character matrices, and supports reading and writing of the data in a range of standard phylogenetic data formats, such as NEXUS, Newick, NeXML, PHYLIP, FASTA, etc. In addition, scripts for performing some useful phylogenetic computations are distributed as part of the libary, such as SumTrees, which summarizes the support for splits or clades given by a posterior sample of phylogenetic trees.
DendroPy runs under any version of Python 2.x greater than Python 2.4 up to, but not including, Python 3.0.
If you have setuptools installed, you can install the latest release of DendroPy directly from the Python Package Index by running:
$ sudo easy_install -U dendropy
Alternatively, if you have pip installed, you can run:
$ sudo pip install dendropy
If you have downloaded the source code distribution archive from the Python Package Index, you can unarchive it and install it from the local source by running:
$ tar -xvzf DendroPy-3.0.0.tar.gz
$ cd DendroPy-3.0.0
$ sudo python setup.py install
The DendroPy Tutorial is a “cookbook”-style tutorial, consisting of annotated practical examples and code walk-throughs, and can be found here:
DendroPy Tutorial
The DendroPy Library Reference documents the modules, classes and methods of the DendroPy library, and can be found here:
DendroPy Library Reference
Much of this information is also readily available from the Python interpreter by invoking help() on an object or name.
Clone the DendroPy Git repository:
$ git clone git://github.com/jeetsukumaran/DendroPy.git
Install DendroPy in development mode:
$ cd DendroPy
$ sudo python setup.py develop
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. 2009. DendroPy Phylogenetic Computing Library Version 3.0.0 (http://packages.python.org/DendroPy/).
If you encounter any problems, errors, crashes etc. while using this program, please let me know at jeet@ku.edu. Please feel free to contact me if you have any other questions, suggestions or comments as well.
The DendroPy library and the DendroPy logo are: Copyright 2009 Jeet Sukumaran and Mark T. Holder.
The DendroPy library is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. The DendroPy library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
Usage of the DendroPy logo, either in whole or in part, is restricted to the authors of the DendroPy library, with limited usage granted to third parties exclusively for the acknowledgement of, or for linking or referring to, the DendroPy library.
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“.
