Methods for comparing 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.
|Author||Thomas Shafee, Ira Cooke|
|Date of publication||2016-09-16 12:55:27|
|Maintainer||Thomas Shafee <email@example.com>|
|License||GPL (>= 2)|
AlignStat: AlignStat: A tool for the statistical comparison of...
compare_alignments: Compare alternative multiple sequence alignments
comparison_alignment: Comparison Alignment
plot_dissimilarity_matrix: A heatmap plot of the dissimilarity matrix of two multiple...
plot_dissimilarity_summary: An area plot summary of the different causes of column...
plot_similarity_heatmap: A heatmap plot of the column identities between two multiple...
plot_similarity_summary: A line plot summary of column similarity between two multiple...
plot_SP_summary: A line plot summary of sum of pairs score between two...
reference_alignment: Reference Alignment