3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>MAFFT Multiple Sequence Alignments</title></head>
21 <p><strong>MAFFT Multiple Sequence Alignments</strong></p>
22 <p> Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "MAFFT version
23 5: improvement in accuracy of multiple sequence alignment." Nucleic Acids
24 Research, 33 511-518</p>
25 <p>MAFFT is a program for the multiple alignment of nucleic acid or protein
26 sequences, and is available from the <strong>Web
27 Service→Alignment→MAFFT Multiple Sequence
28 Alignment</strong> entry in the web services menu.</p>
29 <p>MAFFT utilizes algorithms for spectral correlation to identify
30 homologous regions in a fast-fourier transform representation of each
31 sequence. The Jalview web service runs MAFFT using the
32 '--auto' option which picks optimal parameters
33 for the set of sequences to be aligned.</p>