`arbol` Overview
================

`arbol` is a Python_ package for simple manipulations of phylogenetic trees. 
The intent is to implement several object models for trees, and make it possible
for the package users to easily choose the most natural and efficient data 
structure for their task.

The feature set and development priorities are somewhat idiosyncratic for a 
library.
Development is spurred by the features that I need in my work on CIPRES_ rather
than a concerted effort to expand the functionality of `arbol` itself.
The code in `arbol` is used by the `cipres` python package to implement several 
CIPRES services, but `arbol` does **not** depend on CIPRES. 
Thus, you can install `arbol` by itself.


See the `CIPRES software pages`_ for information about the general CIPRES 
programming effort, and `cipres-python`_ page for information on the python 
face of CIPRES.

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Obtaining and Installing
========================

The code is currently on a branch of the CIPRES svn repository. 
The top of the repository is http://nladr-cvs.sdsc.edu/svn/CIPRES/cipresdev
It is readable using the username **guest** and the password **guest** to login.

The current repository location for `arbol` is
http://nladr-cvs.sdsc.edu/svn/CIPRES/cipresdev/branches/pipres-refactoring/cipres/framework/python/arbol

However `arbol` will soon move to its permanent home at:
http://nladr-cvs.sdsc.edu/svn/CIPRES/cipresdev/trunk/cipres/framework/python/arbol

I plan to release snapshots of the code (not requiring svn) from the 
arbol_ site and at `Cheese Shop`_.
The code uses setuptools_ for easy installation.
It is tested on python 2.4 (but may work on 2.3).

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Road Map
========

* improve the documentation and testing
* alpha release
* improve interoperability with Paul Lewis' Phycas project
* improve Biopython_ interoperability.

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Contributing
============
Currently, all of the code has been written by Mark Holder, but comments and 
contributions are welcome.
Email Mark_ if you would like write-access to the svn repository.
The code is available under either the LGPL_ or a BSD_ license if you would 
like to reuse it.


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See also
=========

* FAQ_
* News_
* ChangeLog_
* Todo_
* Authors_
* Maintainers_
* Thanks_

.. _FAQ: ./FAQ.html
.. _News: ./News.html
.. _ChangeLog: ./ChangeLog.html
.. _Todo: ./Todo.html
.. _Authors: ./Authors.html
.. _Maintainers: ./Maintainers.html
.. _Thanks: ./Thanks.html
.. _LGPL: http://www.opensource.org/licenses/lgpl-license.php
.. _BSD: http://www.opensource.org/licenses/bsd-license.php
.. _LGPL.txt: ./LGPL.txt
.. _Python: http://www.python.org
.. _CIPRES: http://www.phylo.org
.. _CIPRES software pages: http://www.phylo.org/software/SDK/index.php
.. _cipres-python: http://people.ku.edu/~mtholder/cipres-python
.. _arbol: http://people.ku.edu/~mtholder/arbol
.. _Cheese Shop: http://cheeseshop.python.org/pypi
.. _setuptools: http://peak.telecommunity.com/DevCenter/setuptools
.. _Biopython: http://biopython.org/wiki/Main_Page
.. _Mark: mtholder@gmail.com