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The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".
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calculate_Ka_Ks_pipeline Update README.md Mar 2, 2019
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detect_gene_conversion Update README.md Feb 24, 2019
identify_Ks_peaks_by_fitting_GMM Update plot_syntenic_blocks_ks_distri.py May 16, 2019
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README.md Update README.md Jun 16, 2019

README.md

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.

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