Calculate pairwise scores for aligned sequences given a substitution matrix. Optionaly weight for each position in the alignment.

Calculate pairwise scores for aligned sequences given a substitution matrix. Optionaly weight for each position in the alignment.

pairwise_score(seqs, mtx, weight)

Arguments

seqs	A list of character vectors, each represents a sequence in the alignment.
mtx	Substitution matrix as a numeric matrix.
weight	A numeric vector specifying weights for each position in aligned sequences. Same length as sequences 1 and 2.

Value

A NumericMatrix of pairwise scores.