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.
tool.run()
- ipa.treemix
- ipa.pca
- ipa.raxml
- ipa.tetrad
- ipa.structure
- ipa.sratools
- ipa.baba
- ipa.bucky
- ipa.window_extacter
- ipa.treeslider 1
- Required software
- Short Tutorial:
- Write the trees column to a file
- Get Astral
- Run Astral
- Plot astral species tree
- Plot astral species tree with quartet supports
- Required software
- Short Tutorial:
- Longer tutorial
- Cookbook
- What’s next?