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ipyrad: interactive assembly and analysis of RADseq 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.

In this documentation you can learn about the various features of ipyrad (:ref:`Features <features>`), the broader motivation behind its design (:ref:`Ethos <ethos>`), and access detailed :ref:`Tutorials<userguide>`. Several new :ref:`Analysis tools <Analysis tools>` are included with ipyrad, and we are also building a large :ref:`Cookbook` with code for many common downstream analyses.

Got questions about ipyrad? Join the conversation at gitter_.

Documentation

.. toctree::
   :maxdepth: 1

   ethos.rst
   features.rst
   installation.rst

   files.rst
   outline.rst
   parameters.rst
   methods.rst

   userguide.rst
   notebooks.rst
   tutorials.rst
   HPC_Tunnel.rst
   analysis.rst
   citing.rst
   releasenotes.rst
   support.rst
   license.rst

Indices and tables