CascadiaTools worked example: Genetic diversity and population structure (FST, FIS, isolation by distance, DAPC)
Module: popgen-structure

These data are SIMULATED, so the true answer is known. See README_data.md.

To try it:
  1. Unzip this folder somewhere you can find it.
  2. Open the folder in Claude Code (with the CascadiaTools plugin installed).
  3. Paste the prompt below.

Prompt:
I have microsatellite genotypes for coastal tailed frogs from 8 streams (tailed_frog_microsats.csv, two columns per locus, 0 means missing) and the stream coordinates (tailed_frog_sites.csv). Please tell me how genetically diverse each stream is, whether any population is inbred or isolated, how different the streams are and whether that increases with distance, and how many genetic groups there are. I don't code, so please give me a report with figures and explain what it means for management.

The analysis settings used for the published example are in config.yaml.
WALKTHROUGH.md shows every step the agent took and the results.
Website: https://cascadiawildlifelab.org/tools/modules/popgen-structure.html
