Here is summary of what these directories contain:
calculate_Ka_Ks_pipeline/: The pipeline used to compute Ka, Ks, and Ka/Ks for duplicated gene pairs.
compute_pearson_r/: The pipeline used to compute Pearson correlation coefficients (r) between expression profiles of the two gene copies.
detect_gene_conversion/: The pipeline used to detect gene conversion events.
identify_Ks_peaks_by_fitting_GMM/: The pipline used to infer the Ks peaks corresponding to WGD events of different ages by fitting Gaussian Mixture Model (GMM) to Ks distributions.