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Recipes

Draft: This section will collect short worked examples that connect ipyrad2 outputs to specific downstream analyses.

Summary

Recipes will show concrete workflows built from assembled HDF5 data, export tools, and built-in analyses.

This section is especially intended for examples such as:

  • exporting sequence alignments with wex or lex for an external phylogenetic program
  • exporting SNP matrices with snpex for an external clustering or association workflow
  • choosing filtering and missing-data settings that match a specific downstream tool
  • comparing an external-file workflow against a built-in analysis workflow inside ipyrad2

Current Recipes

Status

This section is still growing. More example-driven pages will be added over time.