This file contains teaching resources for users new to computational analysis
The scripts here were used in "Archaeogenetics and the Human Past" (Winter 2023, Moots) 

The tool used in these exercises is smartPCA, part of the EIGENSOFT package
More details here - https://github.com/chrchang/eigensoft/blob/master/POPGEN/README

"EIGENSOFT is copyright by Harvard University and The Broad Institute"
http://www.hsph.harvard.edu/alkes-price/software/ 

EIGENSOFT Frequently Asked Questions:
https://www.hsph.harvard.edu/alkes-price/eigensoft-frequently-asked-questions/

For our class projects, we will be working with the Allen Ancient DNA Resource (AARD)

Link to access AADR:
https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data

Paper and citation for AADR
Mallick, S., Micco, A., Mah, M. et al. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 11, 182 (2024). 
https://doi.org/10.1038/s41597-024-03031-7