Adaptation Dynamics

Code associated to the paper Ament-Velásquez, Gilchrist, et al. (2022). The dynamics of adaptation to stress from standing genetic variation and de novo mutations. Molecular Biology and Evolution: msac242. An earlier version of the manuscript is also in bioRxiv.

There are four main Snakemake pipelines the deal with the variant data, analysis and plotting.

1. varcall_adaptation.smk -- For variant calling (directory Variant_calling)
2. vcf4adaptation_env.smk -- For variant filtering and analysis of de novo mutations (directory Variant_filtering/PerEnvironment/)
3. vcf4adaptation.smk -- For variant filtering and analysis of the standing genetic variation (directory Variant_filtering/AllTogether/)
4. ENAdepthCNV.smk -- For inferring copy number changes in the ENA gene from PoolSeq data

The repository also contains code of Ciaran Gilchrist analysing the phenotypic data.

---

I ran the pipelines in Uppsala University's supercomputer UPPMAX, which has a CentOS Linux operating system with a slurm scheduler. However, they should work fine also in other unix environments.