API: ipyrad analysis tools

The ipyrad-analysis toolkit is a Python interface for taking the output files produced in a ipyrad assembly and running a suite of evolutionary analysis tools with convenient features for filtering for missing data, grouping individuals into populations, dropping samples, and more.

All of these tools share a common syntax making them easy to use without having to worry about creating different input files, or learn new file formats. They are designed for use within Jupyter notebooks, a tool for reproducible science. See the examples below.

# the analysis tools are a subpackage of ipyrad
import ipyrad as ipa

# a large suite of tools are available
tool = ipa.structure(data="./outfiles/data.snps.hdf5")

# all tools share a common syntax for setting params
# and distributing work in parallel.