get_substitute_mtx()
Get the substitution matrix.
pairwise_score()
Calculate pairwise scores for aligned sequences given a substitution matrix. Optionaly weight for each position in the alignment.
parallel_pairwise_score()
Calculate pairwise scores for aligned sequences given a substitution matrix. Optionaly weight for each position in the alignment. Same as `pairwise_score`, except this is parallelized.
seq_to_idx()
Helper function to convert a character vector to an integer vector of positions in substitution matrix.
two_seq_score()
Calculate scores for two aligned sequences given a substitution matrix. Optionaly weight for each position in the alignment.