AlignStat (version 1.3.1)

AlignStat: 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