This Zenodo record archives the version of the eco_evolutionary_factors_and_hgt GitHub repository used for the generation of the horizontal gene transfer (HGT) event dataset and its downstream analyses, associated with the publication “A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer”, published on 5 March 2024 in Nature Ecology & Evolution, 8, 986–998. The pipeline folder contains all scripts used to generate gene trees for each gene cluster and to reconcile these gene trees with the corresponding species trees. The analysis folder contains all statistical analysis scripts used to investigate global trends in HGT.