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_.
.. 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 faq.rst support.rst license.rst