Code repository for analyses conducted in Matschiner et al. (2021)

This code repository is associated with our manuscript entitled "Supergene origin and maintenance in Atlantic cod", which is available from BioRxiv.

More information on the individual analyses can be found in the README files provided in subdirectories (e.g. inversion_detection/README).

Analyses were conducted in the following order:

1. inversion_detection
2. three_taxon_alignments
3. gadidae_time_calibration
4. mito_nuclear_comparison
5. gadidae_phylogenomics
6. cod_phylogenomics
7. demography

Note that the files named run_all.sh that can be found in each src directory (e.g. inversion_detection/src/run_all.sh) are not intended to be executed, but they specify the order in which all other scripts should be executed.