Fig. 2

Plots of the similarity (S), difference (D) and results (R) matrices generated by compare_alignments of defensin protein MSAs (reference = CysBar alignment, comparison = ClustalΩ alignment). a Similarity matrix visualised by the plot_similarity_heatmap function. b Dissimilarity matrix visualised by the plot_dissimilarity_matrix function. c Matches in results matrix visualised by the plot_similarity_summary function. d Merges, splits and shifts in results matrix visualised by the plot_dissimilarity_proportions function