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.
- Genotype calling
- Mapping_sprat_assembly
- i. whole genome alignments between herring and sprat assemblies
- ii. extracting ancestral state from alignments
- Phylogenetic analysis
- Population genomic analyses
- i. Genotype plots
- ii. Local PCA
- iii. Summary stats pixy
- iv. Recombination
- v. SFS
- Transposable elements
- dNdS analysis
Mafalda Sousa Ferreira: sferreira.mafalda [at] gmail [.] com