2 <head><title>MAFFT Multiple Sequence Alignments</title></head>
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4 <p><strong>MAFFT Multiple Sequence Alignments</strong></p>
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5 <p> Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "MAFFT version
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6 5: improvement in accuracy of multiple sequence alignment." Nucleic Acids
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7 Research, 33 511-518</p>
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8 <p>MAFFT is a program for the multiple alignment of nucleic acid or protein
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9 sequences, and is available from the <strong>Web
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10 Service→Alignment→MAFFT Multiple Sequence
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11 Alignment</strong> entry in the web services menu.</p>
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12 <p>MAFFT utilizes algorithms for spectral correlation to identify
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13 homologous regions in a fast-fourier transform representation of each
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14 sequence. The Jalview web service runs MAFFT using the
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15 '--auto' option which picks optimal parameters
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16 for the set of sequences to be aligned.</p>
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