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Analysis Guide

The ipyrad2 analysis tools are a set of subcommands for running common downstream analyses on assembled datasets. Each takes the HDF5 database file as input, and includes a built-in set of options to filter and subsample taxa and sites to address missing data.

Open TODOs

  • Add an overview table covering PCA-family, DAPC, admixture, sNMF, popgen, and converters.