Description Computing statistics Plotting functions
This package contains functions that compare two alternative multiple sequence alignments (MSAs) to determine whether they align homologous residues in the same columns as one another. It then classifies similarities and differences into conserved gaps, conserved sequence, merges, splits or shifts of one MSA relative to the other. Summarising these categories for each MSA column yields information on which sequence regions are agreed upon my both MSAs, and which differ. Several plotting functions enable easily visualisation of the comparison data for analysis.
Use compare_alignments
to calculate statistics comparing two MSAs
Use plot_similarity_heatmap
to view a heatmap comparing the similarity
Use plot_dissimilarity_matrix
to view a matrix of dissimilarity types
Use plot_similarity_summary
to view a summary of column average similarity
Use plot_dissimilarity_summary
to view a summary of column dissimilarity types
Use plot_SP_summary
to view a summary of columnwise sum of pairs scores
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