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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

Coming Soon

  • Downstream analysis tools
  • Quartet-based species tree inference (_tetrad_ program)
  • Introgression analyses (ABBA-BABA tests)
  • Population genetic statistics