ipyrad: Interactive assembly and analysis of RAD-seq data sets
=======================
Welcome to ipyrad, an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.

Quick Install
------------
ipyrad is available through conda with all dependencies included. If you have conda installed you can simply:

    conda install -c ipyrad ipyrad

If you do not have conda you will enjoy our `complete installation instructions <http://ipyrad.readthedocs.io/installation.html>`_.

Documentation
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`Full documentation <http://ipyrad.readthedocs.io>`_ is available on our readthedocs site. There you will find installation instructions, example tutorials, and a full user guide.

Quick link to the `full tutorial <http://ipyrad.readthedocs.io/tutorial_intro_cli.html>`_.

Getting Help
------------
Join the ipyrad gitter channel and ask a question, request a feature, or flame the developers:

.. image:: https://badges.gitter.im/Join%20Chat.svg
   :alt: Join the chat at https://gitter.im/dereneaton/ipyrad
   :target: https://gitter.im/dereneaton/ipyrad?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge

What's new?
-----------

In addition to a command line interface that will be familiar to pyrad users, ipyrad offers an additional way to interact with the data through writing Python scripts that access the ipyrad API. This provides an easier way to construct branching assembly architectures in which data sets are assembled under a number of parameter options. We also include several new analysis 
tools, including __svd4tet__, a program for fast quartet inference and super-tree 
construction. 

License
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GPLv3

Contributors
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+ `Deren Eaton <deren.eaton@yale.edu>`_.  
+ `Isaac Overcast <isaac.overcast@gmail.com>`_.