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annotate seqrequester/src/utility/README.licenses @ 1:1085e094cf5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
author fubar
date Sat, 13 Jul 2024 12:39:06 +0000
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1
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2 This software constitutes a joint work and the contributions of individual
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3 authors are subject to different licenses. Contributions and licenses are
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4 listed in the applicable source files, with specific details on each
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5 individual contribution captured in the revision control system.
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6
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7 --
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8 For all code, except as indicated otherwise:
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9
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10 PUBLIC DOMAIN NOTICE
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12 This software is "United States Government Work" under the terms of the
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13 United States Copyright Act. It was written as part of the authors'
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14 official duties for the United States Government and thus cannot be
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15 copyrighted. This software is freely available to the public for use
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16 without a copyright notice. Restrictions cannot be placed on its present or
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17 future use.
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18
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19 Although all reasonable efforts have been taken to ensure the accuracy and
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20 reliability of the software and associated data, the National Human Genome
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21 Research Institute (NHGRI), National Institutes of Health (NIH) and the
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22 U.S. Government do not and cannot warrant the performance or results that
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23 may be obtained by using this software or data. NHGRI, NIH and the
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24 U.S. Government disclaim all warranties as to performance, merchantability
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25 or fitness for any particular purpose.
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26
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27 Please cite the authors in any work or product based on this material.
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28
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29 --
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30 For Edlib:
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31
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32 The MIT License (MIT)
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33
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34 Copyright (c) 2014 Martin Šošić
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35
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36 Permission is hereby granted, free of charge, to any person obtaining a
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37 copy of this software and associated documentation files (the "Software"),
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38 to deal in the Software without restriction, including without limitation
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39 the rights to use, copy, modify, merge, publish, distribute, sublicense,
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40 and/or sell copies of the Software, and to permit persons to whom the
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41 Software is furnished to do so, subject to the following conditions:
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42
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43 The above copyright notice and this permission notice shall be included in
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44 all copies or substantial portions of the Software.
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45
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46 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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47 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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48 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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49 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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50 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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51 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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52 DEALINGS IN THE SOFTWARE.
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53
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54 --
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55 For the MD5 Message-Digest Algorithm:
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56
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57 Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All rights
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58 reserved.
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59
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60 License to copy and use this software is granted provided that it is
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61 identified as the "RSA Data Security, Inc. MD5 Message-Digest Algorithm" in
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62 all material mentioning or referencing this software or this function.
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63
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64 License is also granted to make and use derivative works provided that such
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65 works are identified as "derived from the RSA Data Security, Inc. MD5
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66 Message-Digest Algorithm" in all material mentioning or referencing the
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67 derived work.
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68
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69 RSA Data Security, Inc. makes no representations concerning either the
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70 merchantability of this software or the suitability of this software for
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71 any particular purpose. It is provided "as is" without express or implied
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72 warranty of any kind.
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73
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74 These notices must be retained in any copies of any part of this
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75 documentation and/or software.
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76
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77 --
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78 For MT19937:
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79
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80 Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura, All
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81 rights reserved.
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82
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83 Redistribution and use in source and binary forms, with or without
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84 modification, are permitted provided that the following conditions are
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85 met:
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86
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87 1. Redistributions of source code must retain the above copyright notice,
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88 this list of conditions and the following disclaimer.
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89
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90 2. Redistributions in binary form must reproduce the above copyright
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91 notice, this list of conditions and the following disclaimer in the
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92 documentation and/or other materials provided with the distribution.
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93
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94 3. The names of its contributors may not be used to endorse or promote
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95 products derived from this software without specific prior written
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96 permission.
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97
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98 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
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99 IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
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100 THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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101 PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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102 CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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103 EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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104 PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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105 PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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106 LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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107 NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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108 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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109
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110 --
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111 For libbacktrace:
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112
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113 Copyright (C) 2012-2016 Free Software Foundation, Inc.
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114
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115 Redistribution and use in source and binary forms, with or without
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116 modification, are permitted provided that the following conditions are met:
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117
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118 (1) Redistributions of source code must retain the above copyright
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119 notice, this list of conditions and the following disclaimer.
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120
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121 (2) Redistributions in binary form must reproduce the above copyright
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122 notice, this list of conditions and the following disclaimer in
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123 the documentation and/or other materials provided with the
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124 distribution.
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125
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126 (3) The name of the author may not be used to endorse or promote
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127 products derived from this software without specific prior
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128 written permission.
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129
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130 THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
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131 IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
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132 OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
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133 NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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134 SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
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135 TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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136 PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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137 LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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138 NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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139 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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140
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141 --
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142 For SSW Library (align-ssw.C and align-ssw.H):
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143
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144 The MIT License
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145
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146 Copyright (c) 2012-2015 Boston College.
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147
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148 Permission is hereby granted, free of charge, to any person obtaining
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149 a copy of this software and associated documentation files (the
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150 "Software"), to deal in the Software without restriction, including
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151 without limitation the rights to use, copy, modify, merge, publish,
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152 distribute, sublicense, and/or sell copies of the Software, and to
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153 permit persons to whom the Software is furnished to do so, subject to
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154 the following conditions:
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155
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156 The above copyright notice and this permission notice shall be
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157 included in all copies or substantial portions of the Software.
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158
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159 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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160 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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161 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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162 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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163 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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164 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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165 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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166 SOFTWARE.
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167
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168
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169 The 2-clause BSD License
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170
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171 Copyright 2006 Michael Farrar.
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172
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173 Redistribution and use in source and binary forms, with or without
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174 modification, are permitted provided that the following conditions are
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175 met:
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176
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177 1. Redistributions of source code must retain the above copyright
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178 notice, this list of conditions and the following disclaimer.
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179
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180 2. Redistributions in binary form must reproduce the above copyright
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181 notice, this list of conditions and the following disclaimer in the
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182 documentation and/or other materials provided with the distribution.
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183
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184 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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185 "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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186 LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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187 A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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188 HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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189 SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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190 LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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191 DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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192 THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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193 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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194 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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195
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196 --
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197 For parasail:
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198
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199 Pairwise Sequence Alignment Library (parasail)
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200
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201 Copyright (c) 2015, Battelle Memorial Institute
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202
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203 1. Battelle Memorial Institute (hereinafter Battelle) hereby grants
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204 permission to any person or entity lawfully obtaining a copy of this
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205 software and associated documentation files (hereinafter “the
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206 Software”) to redistribute and use the Software in source and binary
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207 forms, with or without modification. Such person or entity may use,
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208 copy, modify, merge, publish, distribute, sublicense, and/or sell
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209 copies of the Software, and may permit others to do so, subject to
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210 the following conditions:
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211
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212 - Redistributions of source code must retain the above copyright
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213 notice, this list of conditions and the following disclaimers.
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214
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215 - Redistributions in binary form must reproduce the above copyright
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216 notice, this list of conditions and the following disclaimer in
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217 the documentation and/or other materials provided with the
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218 distribution.
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219
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220 - Other than as used herein, neither the name Battelle Memorial
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221 Institute or Battelle may be used in any form whatsoever without
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222 the express written consent of Battelle.
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223
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224 - Redistributions of the software in any form, and publications
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225 based on work performed using the software should include the
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226 following citation as a reference:
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227
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228 Daily, Jeff. (2016). Parasail: SIMD C library for global,
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229 semi-global, and local pairwise sequence alignments. *BMC
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230 Bioinformatics*, 17(1), 1-11. doi:10.1186/s12859-016-0930-z
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231
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232 2. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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233 "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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234 LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
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235 FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL BATTELLE
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236 OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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237 SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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238 LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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239 USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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240 ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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241 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
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242 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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243 SUCH DAMAGE.
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244