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update readme to be more official
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isaacovercast authored Jun 10, 2016
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ipyrad (In development)
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.

.. 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

Interactive assembly and analysis of RAD-seq data sets.
Quick Install
------------
ipyrad is available through conda with all dependencies included. If you have conda installed you can simply:

Tutorials
---------
conda install -c ipyrad ipyrad

Documentation is in the works_. There you can find installation instructions,
example tutorials, and a full user guide. Much more on the way.
If you do not have conda you will enjoy our `complete installation instructions <http://ipyrad.readthedocs.io/installation.html>`_.

.. _works: http://ipyrad.readthedocs.io
Documentation
---------
`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>`_.

Installation
Getting Help
------------
ipyrad is available through conda (and pip) with all dependencies included.
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 (docs coming).

construction.

License
-------
GPLv3


Contributors
------------
+ `Deren Eaton <[email protected]>`_.
+ `Isaac Overcast <[email protected]>`_.





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