• similarity measure
• sequence alphabet
• distance measure
• hamming distance
• edit operation
• scoring function
• score
• edit distance
• pairwise alignment
• distance matrix
• block-indel
• local alignment
• local similarity
• profile alignment
• multiple alignment
• sum-of-pairs score
• dynamic programming hyperlattice
• carrillo-lipman bound
• alignment along a tree
• scoring along a tree
• structurally verified alignment
• msa alignment
• clustal alignment