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annotate mafft/readme @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 -----------------------------------------------------------------------
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2 MAFFT: a multiple sequence alignment program
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3 version 7.221beta, 2015/04/16
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4
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5 http://mafft.cbrc.jp/alignment/software/
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6 kazutaka.katoh@aist.go.jp
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7 -----------------------------------------------------------------------
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8
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9 1. COMPILE
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10 % cd core
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11 % make clean
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12 % make
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13 % cd ..
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14
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15 To enable multithreading (linux only),
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16 % cd core
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17 Uncomment line 8 of Makefile,
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18 ENABLE_MULTITHREAD = -Denablemultithread
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19 % make clean
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20 % make
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21 % cd ..
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22
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23 If you have the './extensions' directory, which is for RNA alignments,
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24 % cd extensions
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25 % make clean
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26 % make
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27 % cd ..
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28
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29
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30 2. INSTALL (select 2a or 2b [])
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31 2a. Install as root
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32 # cd core
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33 # make install
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34 # cd ..
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35
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36 If you have the './extensions' directory,
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37 # cd extensions
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38 # make install
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39 # cd ..
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40
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41 By this procedure (2a), programs are installed into
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42 /usr/local/bin/. Some binaries, which are not directly
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43 used by a user, are installed into /usr/local/libexec/mafft/.
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44
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45 If the MAFFT_BINARIES environment variable is set to /somewhare/else/,
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46 the binaries in the /somewhere/else/ directory are used, instead
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47 of those in /usr/local/libexec/mafft/.
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48
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49 2b. Install without being root
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50 % cd core/
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51 Edit the first line of Makefile
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52 From:
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53 PREFIX = ${PKGDIR}/usr/local
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54 To:
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55 PREFIX = /home/your_home/somewhere
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56
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57 Edit the third line of Makefile
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58 From:
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59 BINDIR = $(PREFIX)/bin
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60 To:
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61 BINDIR = /home/your_home/bin
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62 (or elsewhere in your command-search path)
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63 % make clean
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64 % make
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65 % make install
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66
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67 If you have the './extensions' directory,
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68 % cd ../extensions/
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69 Edit the first line of Makefile
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70 From:
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71 PREFIX = ${PKGDIR}/usr/local
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72 To:
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73 PREFIX = /home/your_home/somewhere
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74 % make clean
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75 % make
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76 % make install
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77
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78 The MAFFT_BINARIES environment variable *must not be* set.
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79
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80 If the MAFFT_BINARIES environment variable is set to /somewhare/else/,
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81 it overrides the setting of PREFIX (/home/your_home/somewhere/ in the
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82 above example) in Makefile.
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83
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84 3. CHECK
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85 % cd test
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86 % rehash # if necessary
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87 % mafft sample > test.fftns2 # FFT-NS-2
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88 % mafft --maxiterate 100 sample > test.fftnsi # FFT-NS-i
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89 % mafft --globalpair sample > test.gins1 # G-INS-1
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90 % mafft --globalpair --maxiterate 100 sample > test.ginsi # G-INS-i
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91 % mafft --localpair sample > test.lins1 # L-INS-1
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92 % mafft --localpair --maxiterate 100 sample > test.linsi # L-INS-i
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93 % diff test.fftns2 sample.fftns2
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94 % diff test.fftnsi sample.fftnsi
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95 % diff test.gins1 sample.gins1
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96 % diff test.ginsi sample.ginsi
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97 % diff test.lins1 sample.lins1
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98
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99 If you have the './extensions' directory,
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100 % mafft-qinsi samplerna > test.qinsi # Q-INS-i
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101 % mafft-xinsi samplerna > test.xinsi # X-INS-i
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102 % diff test.qinsi samplerna.qinsi
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103 % diff test.xinsi samplerna.xinsi
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104
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105 If you use the multithread version, the results of iterative refinement
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106 methods (*-*-i) are not always identical. Try this test with the single-
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107 thread mode (--thread 0).
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108
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109
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110 4. INPUT FORMAT
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111 fasta format.
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112
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113 The type of input sequences (nucleotide or amino acid) is
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114 automatically recognized based on the frequency of A, T, G, C, U and N.
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115
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116
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117 5. USAGE
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118 % /usr/local/bin/mafft input > output
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119
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120 See also http://mafft.cbrc.jp/alignment/software/
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121
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122
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123 6. UNINSTALL
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124 # rm -r /usr/local/libexec/mafft
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125 # rm /usr/local/bin/mafft
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126 # rm /usr/local/bin/fftns
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127 # rm /usr/local/bin/fftnsi
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128 # rm /usr/local/bin/nwns
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129 # rm /usr/local/bin/nwnsi
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130 # rm /usr/local/bin/linsi
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131 # rm /usr/local/bin/ginsi
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132 # rm /usr/local/bin/mafft-*
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133 # rm /usr/local/share/man/man1/mafft*
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134
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135
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136 7. LICENSE
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137 See the './license' file.
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138
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139 If you have the extensions, see also the './license.extensions' file,