AlignStat (version 1.3.1)

compare_alignments: Compare alternative multiple sequence alignments

Description

Compare alternative multiple sequence alignments

Usage

compare_alignments(ref, com, SP = FALSE, CS = FALSE)

Arguments

ref

The reference MSA (in fasta, clustal, msf, phylip or mase format)

com

The MSA to compare (in fasta, clustal, msf, phylip or mase format)

SP

Optionally also compute sum of pairs scores (default=FALSE)

CS

Optionally also compute total column score (default=FALSE)

Value

Generates an object of class "pairwise alignment comparison" (PAC), providing the optimal pairwise column alignment of two alternative MSAs of the same sequences, and summary statistics of the differences between them. The details of the PAC output components are as follows:

• reference_P The numbered character matrix of the reference alignment
• comparison_Q The numbered character matrix of the comparison alignment
• results_R The results summary matrix (containing column averages of match, gapcon, merge, split, shift)
• similarity_S The similarity matrix between the reference and comparison alignment columns
• dissimilarity_D The dissimilarity matrix between the reference and comparison (containing match, gapcon, merge, split, shift)
• dissimilarity_simple The dissimilarity matrix with categories stacked into a single 2D matrix
• columnmatch The column of the comparison alignment with the highest final match score
• cys The proportion of cysteines (relevant for cysteine rich proteins)
• reflen The length of the reference alignment
• comlen The length of the comparison alignment
• refcon The consensus sequence of the reference alignment
• comcon The consensus sequence of the comparison alignment
• similarity_score The overall similarity score
• column_score The proportion of columns that are fully identical between the reference and comparison MSAs and related data (optional)
• sum_of_pairs The sum of pairs score and related data (optional)

Examples

data(reference_alignment)
data(comparison_alignment)
PAC <- compare_alignments(reference_alignment,comparison_alignment)