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2 MAFFT: a multiple sequence alignment program
3 version 6.713beta, 2009/09/24
5 http://align.bmr.kyushu-u.ac.jp/mafft/software/
6 katoh@bioreg.kyushu-u.ac.jp
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15 If you have the './extensions' directory, which is for RNA alignments,
22 2. INSTALL (select one procedure from 2a, 2b and 2c)
28 If you have the './extensions' directory,
33 By this procedure (2a), programs are installed into
34 /usr/local/bin/ and some binaries are installed into
35 /usr/local/lib/mafft/.
37 If you want to install the binaries to a different directory
38 than /usr/local/lib/mafft/, select either of the following
39 two procedure (2b and 2c).
41 2b. Install without being root
42 % cp ./binaries/* /somewhere/else/
44 In this case (2b), you *have to set* the MAFFT_BINARIES environment
45 variable to point to the directory where the binaries are.
46 % setenv MAFFT_BINARIES /somewhere/else/ # for csh, tcsh
47 $ export MAFFT_BINARIES=/somewhere/else/ # for sh, bash
49 2c. Install without being root
51 Edit the first line of Makefile
55 PREFIX = /home/your_home/somewhere
60 If you have the './extensions' directory,
62 Edit the first line of Makefile
66 PREFIX = /home/your_home/somewhere
71 In this case (2c), the MAFFT_BINARIES environment variable
77 % rehash # if necessary
78 % setenv MAFFT_BINARIES /where/binaries/were/installed # if necessary
79 % mafft sample > test.fftns2 # FFT-NS-2
80 % mafft --maxiterate 100 sample > test.fftnsi # FFT-NS-i
81 % mafft --globalpair sample > test.gins1 # G-INS-1
82 % mafft --globalpair --maxiterate 100 sample > test.ginsi # G-INS-i
83 % mafft --localpair sample > test.lins1 # L-INS-1
84 % mafft --localpair --maxiterate 100 sample > test.linsi # L-INS-i
85 % diff test.fftns2 sample.fftns2
86 % diff test.fftnsi sample.fftnsi
87 % diff test.gins1 sample.gins1
88 % diff test.ginsi sample.ginsi
89 % diff test.lins1 sample.lins1
91 If you have the './extensions' directory,
92 % mafft-qinsi samplerna > test.qinsi # Q-INS-i
93 % mafft-xinsi samplerna > test.xinsi # X-INS-i
94 % diff test.linsi sample.linsi
95 % diff test.qinsi sample.qinsi
96 % diff test.xinsi sample.xinsi
102 The type of input sequences (nucleotide or amino acid) is
103 automatically recognized based on the frequency of A, T, G, C, U and N.
107 % /usr/local/bin/mafft input > output
109 See also http://align.bmr.kyushu-u.ac.jp/mafft/software/
113 # rm -r /usr/local/lib/mafft
114 # rm /usr/local/bin/mafft
115 # rm /usr/local/bin/fftns
116 # rm /usr/local/bin/fftnsi
117 # rm /usr/local/bin/nwns
118 # rm /usr/local/bin/nwnsi
119 # rm /usr/local/bin/linsi
120 # rm /usr/local/bin/ginsi
121 # rm /usr/local/bin/mafft-*
125 See the './license' file.
127 If you have the extensions, see the './license.extensions' file,