What does ipyrad do?
ipyrad_ is a toolbox for assembly and analysis of RAD-seq type genomic data sets. Notably, it has four :ref:`assembly methods<assembly_methods>` by which to assemble data: denovo, reference, reference addition, and reference subtraction. Assembled data sets are created in a variety of :ref:`output formats<full_output_formats>`, facilitating downstream genomic analyses for both population genetic and phylogenetic studies. ipyrad_ also includes methods for visualizing and analyzing data and results.
How is it different from pyrad?
ipyrad_ is a complete re-write of pyrad_ with an expanded focus on speed and flexibility. While we continue in the minimalist :ref:`ethos<ethos>` of pyrad_, which emphasized a simple installation procedure and ease-of-use, ipyrad_ offers many new features, and is now easily extensible to new data types and models through its Python :ref:`API<API>`.
Major New Features in ipyrad
- New :ref:`assembly methods<assembly_methods>`: de novo and reference-based methods.
- Improved :ref:`checkpointing<checkpointing>`. Interrupted jobs are easily restarted.
- Much faster code (speed comparisons forthcoming with publication).
- State of the art parallel implementation (ipyparallel) for running on computing clusters.
- Easy installation: all dependencies are included during :ref:`installation<installation>`.
- Downstream analysis tools
- Quartet-based species tree inference (_tetrad_ program)
- Introgression analyses (ABBA-BABA tests)
- Population genetic statistics