This repository contains the scripts to produce the data, figures, tables and perform statistical analysis included in the manuscript Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures in a Jupyter Notebook document (GenerationTimeFiguresAndTables.ipynb).
To generate the Data1_archaicfragments.txt and Data3_HGDParchaicfragments.txt dataset, we followed the documentation on https://github.com/LauritsSkov/Introgression-detection, with different sets of samples detailed in the manuscript.
To generate the Data2_mutation_spectrum.txt, we run the scripts in MutationAccumulation. For a detailed description, check the derived_alleles.ipynb Jupyter Notebook.