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Distance matrix
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===== MAFFT ===== Multiple alignment using fast Fourier transform (MAFFT) is a program with an algorithm based on progressive alignment, and it offers various multiple alignment strategies. First, MAFFT constructs a distance matrix based on the number of shared 6-tuples. Second, it builds the guide tree based on the previous matrix. Third, it clusters the sequences with the help of the [[fast Fourier transform]] and starts the alignment. Based on the new alignment, it reconstructs the guide tree and align again.
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