When there are more than two inputs to this technique, the output is ideally stored in Stockholm format, though the simpler (*) FASTA format is more commonly used.
This task is related to, but distinct from, computing the Levenshtein distance, and one algorithm for doing it constructs a scoring matrix based on a gap-scoring scheme and then backtracks from the final cell to produce an output. That dynamic programming algorithm is the Smith-Waterman algorithm, which is a refinement of the earlier Needleman-Wunsch algorithm. When there are more than two inputs to this technique, the output is ideally stored in Stockholm format, though the simpler (*) FASTA format is more commonly used. Gap-scoring schemes for doing this apply a penalty to indels, which correspond to frame shifts. One program used to perform this technique is ClustalW, and the output of this technique may be used to construct phylogenetic trees. For 10 points, name this technique in bioinformatics in which sequences of nucleotides or amino acids are arranged with respect to one another in such a way as to maximize locations at which the lists match.
This task is related to, but distinct from, computing the Levenshtein distance, and one algorithm for doing it constructs a scoring matrix based on a gap-scoring scheme and then backtracks from the final cell to produce an output.
sequence alignment [or word forms; accept things like "aligning sequences of nucleotides" and so forth; accept just alignment after "sequences" is read]