readme
1-----------------------------------------------------------------------
2 MAFFT: a multiple sequence alignment program
3 version 7.267beta, 2015/12/09
4
5 http://mafft.cbrc.jp/alignment/software/
6 kazutaka.katoh@aist.go.jp
7-----------------------------------------------------------------------
8
91. COMPILE
10 % cd core
11 % make clean
12 % make
13 % cd ..
14
15 To enable multithreading (linux only),
16 % cd core
17 Uncomment line 8 of Makefile,
18 ENABLE_MULTITHREAD = -Denablemultithread
19 % make clean
20 % make
21 % cd ..
22
23 If you have the './extensions' directory, which is for RNA alignments,
24 % cd extensions
25 % make clean
26 % make
27 % cd ..
28
29
302. INSTALL (select 2a or 2b [])
312a. Install as root
32 # cd core
33 # make install
34 # cd ..
35
36 If you have the './extensions' directory,
37 # cd extensions
38 # make install
39 # cd ..
40
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/.
44
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/.
48
492b. Install without being root
50 % cd core/
51 Edit the first line of Makefile
52 From:
53 PREFIX = ${PKGDIR}/usr/local
54 To:
55 PREFIX = /home/your_home/somewhere
56
57 Edit the third line of Makefile
58 From:
59 BINDIR = $(PREFIX)/bin
60 To:
61 BINDIR = /home/your_home/bin
62 (or elsewhere in your command-search path)
63 % make clean
64 % make
65 % make install
66
67 If you have the './extensions' directory,
68 % cd ../extensions/
69 Edit the first line of Makefile
70 From:
71 PREFIX = ${PKGDIR}/usr/local
72 To:
73 PREFIX = /home/your_home/somewhere
74 % make clean
75 % make
76 % make install
77
78 The MAFFT_BINARIES environment variable *must not be* set.
79
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.
83
843. CHECK
85 % cd test
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
98
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
104
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).
108
109
1104. INPUT FORMAT
111 fasta format.
112
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.
115
116
1175. USAGE
118 % /usr/local/bin/mafft input > output
119
120See also http://mafft.cbrc.jp/alignment/software/
121
122
1236. UNINSTALL
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*
134
135
1367. LICENSE
137 See the './license' file.
138
139 If you have the extensions, see also the './license.extensions' file,
140