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.
tool.run()ipa.vcf_to_hdf5 <cookbook-vcf2hdf5.ipynb> ipa.treemix <cookbook-treemix.ipynb> ipa.pca <cookbook-pca.ipynb> ipa.raxml <cookbook-raxml.ipynb> ipa.mrbayes <cookbook-mrbayes.ipynb> ipa.tetrad <cookbook-tetrad.ipynb> ipa.structure <cookbook-structure.ipynb> ipa.sratools <cookbook-sratools.ipynb> ipa.baba <cookbook-abba-baba.ipynb> ipa.bucky <cookbook-bucky.ipynb> ipa.window_extacter <cookbook-window_extracter.ipynb>