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2 MAFFT: a multiple sequence alignment program
3 version 6.857beta, 2011/05/30
5 http://mafft.cbrc.jp/alignment/software/
6 kazutaka.katoh@aist.go.jp
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15 To enable multithreading (linux only),
17 Uncomment line 8 of Makefile,
18 ENABLE_MULTITHREAD = -Denablemultithread
23 If you have the './extensions' directory, which is for RNA alignments,
30 2. INSTALL (select 2a or 2b [])
36 If you have the './extensions' directory,
41 By this procedure (2a), programs are installed into
42 /usr/local/bin/. Some binaries, which are not directly
43 used by a user, are installed into /usr/local/libexec/mafft/.
45 If the MAFFT_BINARIES environment variable is set to /somewhare/else/,
46 the binaries in the /somewhere/else/ directory are used, instead
47 of those in /usr/local/libexec/mafft/.
49 2b. Install without being root
51 Edit the first line of Makefile
53 PREFIX = ${PKGDIR}/usr/local
55 PREFIX = /home/your_home/somewhere
57 Edit the third line of Makefile
59 BINDIR = $(PREFIX)/bin
61 BINDIR = /home/your_home/bin
62 (or elsewhere in your command-search path)
67 If you have the './extensions' directory,
69 Edit the first line of Makefile
71 PREFIX = ${PKGDIR}/usr/local
73 PREFIX = /home/your_home/somewhere
78 The MAFFT_BINARIES environment variable *must not be* set.
80 If the MAFFT_BINARIES environment variable is set to /somewhare/else/,
81 it overrides the setting of PREFIX (/home/your_home/somewhere/ in the
82 above example) in Makefile.
86 % rehash # if necessary
87 % mafft sample > test.fftns2 # FFT-NS-2
88 % mafft --maxiterate 100 sample > test.fftnsi # FFT-NS-i
89 % mafft --globalpair sample > test.gins1 # G-INS-1
90 % mafft --globalpair --maxiterate 100 sample > test.ginsi # G-INS-i
91 % mafft --localpair sample > test.lins1 # L-INS-1
92 % mafft --localpair --maxiterate 100 sample > test.linsi # L-INS-i
93 % diff test.fftns2 sample.fftns2
94 % diff test.fftnsi sample.fftnsi
95 % diff test.gins1 sample.gins1
96 % diff test.ginsi sample.ginsi
97 % diff test.lins1 sample.lins1
99 If you have the './extensions' directory,
100 % mafft-qinsi samplerna > test.qinsi # Q-INS-i
101 % mafft-xinsi samplerna > test.xinsi # X-INS-i
102 % diff test.qinsi samplerna.qinsi
103 % diff test.xinsi samplerna.xinsi
105 If you use the multithread version, the results of iterative refinement
106 methods (*-*-i) are not always identical. Try this test with the single-
107 thread mode (--thread 0).
113 The type of input sequences (nucleotide or amino acid) is
114 automatically recognized based on the frequency of A, T, G, C, U and N.
118 % /usr/local/bin/mafft input > output
120 See also http://mafft.cbrc.jp/alignment/software/
124 # rm -r /usr/local/libexec/mafft
125 # rm /usr/local/bin/mafft
126 # rm /usr/local/bin/fftns
127 # rm /usr/local/bin/fftnsi
128 # rm /usr/local/bin/nwns
129 # rm /usr/local/bin/nwnsi
130 # rm /usr/local/bin/linsi
131 # rm /usr/local/bin/ginsi
132 # rm /usr/local/bin/mafft-*
133 # rm /usr/local/share/man/man1/mafft*
137 See the './license' file.
139 If you have the extensions, see also the './license.extensions' file,