This repository contains the analysis pipeline used in the study Comparison of the Distribution of Fitness Effects Across Primates. The project investigates how DFEs vary across 38 catarrhine primates and to what extent interspecific differences are explained by variation in effective population size Nₑ.

The workflow performs:

• SFS construction – VCF parsing, degeneracy annotation (0-fold / 4-fold), and ancestral allele inference using fastDFE
• DFE inference – estimation of DFEs with gamma–exponential and discrete models using fastDFE
• Comparative analyses – associations between DFE properties and Nₑ, including phylogenetic regressions

DFE estimates are provided in the directory results/tables/dfe/catarrhini/, and site-frequency spectra in results/sfs/comp/original_ref/catarrhini/.

Code and results for the phylogenetic regression analyses are available in the GitHub repository
tbata/PLS_DFE.

The analysis is implemented as a Snakemake workflow.

Structure:

• workflow/
  • Snakefile – main workflow entry point
  • scripts/ – Python scripts used by rules
  • envs/ – conda environment definitions
• resources/ – reference data
• results/ – workflow outputs