jeetsukumaran / DendroPy

Introduction
============
DendroPy is a Python library for phylogenetic scripting, simulation, data processing and data manipulation, with its 
primary home page at:
    https://packages.python.org/DendroPy/
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.
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 <https://pypi.python.org/pypi/setuptools>`_ installed, you can install the latest public release 
of DendroPy directly from the `Python Package Index <https://pypi.python.org/pypi/DendroPy/>`_ by running::
    $ sudo easy_install -U dendropy
Alternatively, if you have `pip <https://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 <https://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:
    https://packages.python.org/DendroPy/tutorial/index.html
While the API reference can be found here:
    https://packages.python.org/DendroPy/library/index.html
Source Code Repository
======================
The DendroPy source code is version-controlled using `Git <https://git-scm.com/>`_, and the `DendroPy Git repository 
<https://github.com/jeetsukumaran/DendroPy>`_ can be cloned by running::
    $ git clone git://github.com/jeetsukumaran/DendroPy.git
More Information
=================
More information, including documentation, tutorials, citation, license, etc. can be found in the `DendroPy home page 
<https://packages.python.org/DendroPy/>`_:
    https://packages.python.org/DendroPy/