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:
- Sequence processing and genotyping
- PCAs
- 1.1 Full 99 dataset (without outgroups)
- 1.2 Individual lakes
- RAxML
- Admixture
- Dsuites - dataset-wide f-branch stats
- GWAS
- 5.1 Gill raker count
- 5.2 Sex
- parallel study
- 6.1 PCA
- 6.2 Fst
- 6.3 CSS
- 6.4 outlier analysis
- f4 statistics
- KEGG differences for fst outlier overlaps