This repository contains all code associated with De-Kayne et al. 2022 - https://www.nature.com/articles/s41467-022-32181-8

This repository has a DOI -

Please see the Wiki here: https://github.com/RishiDeKayne/Alpine_whitefish_WGS/wiki for a more detailed overview of each script Scripts span the following analyses:

0. Sequence processing and genotyping
1. PCAs

• 1.1 Full 99 dataset (without outgroups)
• 1.2 Individual lakes

2. RAxML
3. Admixture
4. Dsuites - dataset-wide f-branch stats
5. GWAS

• 5.1 Gill raker count
• 5.2 Sex

6. parallel study

• 6.1 PCA
• 6.2 Fst
• 6.3 CSS
• 6.4 outlier analysis

7. f4 statistics
8. KEGG differences for fst outlier overlaps