| 1 | MAFFT |
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| 2 | |
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| 3 | DESCRIPTION |
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| 4 | |
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| 5 | MAFFT is a multiple sequence alignment program for unix-like |
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| 6 | operating systems. It offers a range of multiple alignment |
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| 7 | methods, L-INS-i (accurate; for alignment of <âŒ200 sequences), |
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| 8 | FFT-NS-2 (fast; for alignment of <âŒ10,000 sequences), etc. |
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| 9 | |
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| 10 | See http://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html |
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| 11 | for a detailed explanation of the algorithms. |
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| 12 | |
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| 13 | Copyright (c) 2009 Kazutaka Katoh |
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| 14 | |
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| 15 | Accuracy-oriented methods: |
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| 16 | |
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| 17 | L-INS-i |
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| 18 | Probably most accurate; recommended for <200 sequences; |
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| 19 | iterative refinement method incorporating local pairwise |
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| 20 | alignment information. |
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| 21 | |
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| 22 | G-INS-i |
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| 23 | Suitable for sequences of similar lengths; |
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| 24 | recommended for <200 sequences; iterative refinement |
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| 25 | method incorporating global pairwise alignment information. |
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| 26 | |
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| 27 | E-INS-i |
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| 28 | Suitable for sequences containing large unalignable regions; |
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| 29 | recommended for <200 sequences. |
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| 30 | |
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| 31 | |
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| 32 | Speed-oriented methods: |
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| 33 | |
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| 34 | FFT-NS-i |
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| 35 | Iterative refinement method; two cycles only. |
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| 36 | |
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| 37 | FFT-NS-2 |
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| 38 | Fast; progressive method. |
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| 39 | |
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| 40 | NW-NS-i |
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| 41 | Iterative refinement method without FFT approximation; |
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| 42 | two cycles only. |
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| 43 | |
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| 44 | NW-NS-2 |
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| 45 | Fast; progressive method without the FFT approximation. |
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| 46 | |
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| 47 | LICENSE |
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| 48 | MAFFT: multiple sequence alignment program |
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| 49 | Copyright (c) 2009 Kazutaka Katoh |
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| 50 | |
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| 51 | Redistribution and use in source and binary forms, |
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| 52 | with or without modification, are permitted provided |
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| 53 | that the following conditions are met: |
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| 54 | |
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| 55 | Redistributions of source code must retain the |
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| 56 | above copyright notice, this list of conditions |
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| 57 | and the following disclaimer. Redistributions in |
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| 58 | binary form must reproduce the above copyright |
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| 59 | notice, this list of conditions and the following |
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| 60 | disclaimer in the documentation and/or other |
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| 61 | materials provided with the distribution. |
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| 62 | |
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| 63 | The name of the author may not be used to endorse |
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| 64 | or promote products derived from this software without |
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| 65 | specific prior written permission. |
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| 66 | |
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| 67 | THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" |
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| 68 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, |
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| 69 | BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF |
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| 70 | MERCHANTABILITY AND FITNESS FOR A PARTICULAR |
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| 71 | PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE |
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| 72 | AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, |
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| 73 | INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL |
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| 74 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT |
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| 75 | OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, |
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| 76 | OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED |
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| 77 | AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, |
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| 78 | STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR |
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| 79 | OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF |
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| 80 | THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY |
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| 81 | OF SUCH DAMAGE. |
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