ipyrad is a toolbox for assembly and analysis of RAD-seq type genomic data sets. Notably, it has four 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 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.
ipyrad is a complete re-write of pyrad with an expanded focus on speed and flexibility. While we continue in the minimalist 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 API<API>.
Major New Features in ipyrad ----------------------* New assembly methods<assembly_methods>: de novo and reference-based methods. * Improved 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 installation<installation>.
- Downstream analysis tools
- Quartet-based species tree inference (_tetrad program)
- Introgression analyses (ABBA-BABA tests)
- Population genetic statistics