Scripts_for_GB

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.

Citation

Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH: Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants. Genome Biology 2019, 20:38.