Here I document the code used for analyses of short-read whole genome data to study the evolution of Atlantic herring inversions from The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring.

1. Genotype calling
2. Mapping_sprat_assembly
   • i. whole genome alignments between herring and sprat assemblies
   • ii. extracting ancestral state from alignments
3. Phylogenetic analysis
4. Population genomic analyses
   • i. Genotype plots
   • ii. Local PCA
   • iii. Summary stats pixy
   • iv. Recombination
   • v. SFS
5. Transposable elements
6. dNdS analysis

Mafalda Sousa Ferreira: sferreira.mafalda [at] gmail [.] com