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-<head><title>MAFFT Alignment</title></head>\r
+<head><title>MAFFT Multiple Sequence Alignments</title></head>\r
<body>\r
-<p><strong>MAFFT Alignments</strong></p>\r
-<p>MAFFT is a program for the alignment of many protein sequences.</p>\r
+<p><strong>MAFFT Multiple Sequence Alignments</strong></p>\r
<p> Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "MAFFT version \r
5: improvement in accuracy of multiple sequence alignment." Nucleic Acids \r
Research, 33 511-518</p>\r
-<p> This alignment method is applied to the selected region, if any, or the whole \r
- sequence set when the <strong>Web Service→Alignment→MAFFT Multiple \r
- Sequence Alignment</strong> menu item is selected. </p>\r
+<p>MAFFT is a program for the multiple alignment of nucleic acid or protein\r
+sequences, and is available from the <strong>Web\r
+Service→Alignment→MAFFT Multiple Sequence\r
+Alignment</strong> entry in the web services menu.</p>\r
+<p>MAFFT utilizes algorithms for spectral correlation to identify\r
+homologous regions in a fast-fourier transform representation of each\r
+sequence. The Jalview web service runs MAFFT using the\r
+'--auto' option which picks optimal parameters\r
+for the set of sequences to be aligned.</p>\r
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