R: AlignStat: A tool for the statistical comparison of...
AlignStat
R Documentation
AlignStat: A tool for the statistical comparison of alternative multiple sequence alignments
Description
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.
Computing statistics
Use compare_alignments to calculate statistics comparing two MSAs
Plotting functions
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