Biases in demographic modelling affect our understanding of recent divergence

This repository incorporates data and scripts associated with the paper "Biases in demographic modelling affect our understanding of recent divergence" published in Molecular Biology and Evolution (doi: 10.1093/molbev/msab047 ). 

Included in the repository are the following compressed folders: 

1. Alignment_and_SNP_Calling.zip. Contains bioinformatic pipelines to align raw data (available in GenBank from Bioproject PRJNA699405) and generate BAM  and VCF files necessary for further analyses. Several VCF files are also included.
2. SFS.zip. Contains scripts to generate the 2d-SFS for demographic analyses of empirical data. Includes also input SNP files for moments.
3. pi_dxy.zip. This compressed folder contains a bash script to generate 1d-SFS and 2d-SFS in windows across the genome, and R scripts to derive summary statistics from those (\(\pi\), \(\theta\), \(d_{xy}\), Tajima's \(D\)) as well as the results (SFS and summary statistics in windows)
4. PCANGSD.zip. Contains arguments to generate the input file (in beagle format) for PCangsd, results from PCangsd (covariance matrix and selection test statistics) and a R script to plot a PCA. 
5. Stairway_Plots.zip. Contains blueprint files to run StairwayPlots and results. 
6. Simulations.zip. Contains commands to run all simulations, dadi and moments models for inference, results and some R scripts to reproduce plots. 
7. Moments_models.zip. Contains the one-population and two-population models for moments that we designed for this study. 
8. Moments_results.zip. Contains results from demographic models optimized for the empirical data, as well as scripts and results from Likelihood Ratio Tests and estimation of uncertainties using the Godambe Information Matrix. 

Please note that most of these scripts and models are also available from GitHub (https://github.com/Nopaoli/Demographic-Modelling) .