1 2This software constitutes a joint work and the contributions of individual 3authors are subject to different licenses. Contributions and licenses are 4listed in the applicable source files, with specific details on each 5individual contribution captured in the revision control system. 6 7-- 8For all code, except as indicated otherwise: 9 10 PUBLIC DOMAIN NOTICE 11 12 This software is "United States Government Work" under the terms of the 13 United States Copyright Act. It was written as part of the authors' 14 official duties for the United States Government and thus cannot be 15 copyrighted. This software is freely available to the public for use 16 without a copyright notice. Restrictions cannot be placed on its present or 17 future use. 18 19 Although all reasonable efforts have been taken to ensure the accuracy and 20 reliability of the software and associated data, the National Human Genome 21 Research Institute (NHGRI), National Institutes of Health (NIH) and the 22 U.S. Government do not and cannot warrant the performance or results that 23 may be obtained by using this software or data. NHGRI, NIH and the 24 U.S. Government disclaim all warranties as to performance, merchantability 25 or fitness for any particular purpose. 26 27 Please cite the authors in any work or product based on this material. 28 29-- 30For Edlib: 31 32 The MIT License (MIT) 33 34 Copyright (c) 2014 Martin Šošić 35 36 Permission is hereby granted, free of charge, to any person obtaining a 37 copy of this software and associated documentation files (the "Software"), 38 to deal in the Software without restriction, including without limitation 39 the rights to use, copy, modify, merge, publish, distribute, sublicense, 40 and/or sell copies of the Software, and to permit persons to whom the 41 Software is furnished to do so, subject to the following conditions: 42 43 The above copyright notice and this permission notice shall be included in 44 all copies or substantial portions of the Software. 45 46 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 47 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 48 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 49 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 50 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 51 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 52 DEALINGS IN THE SOFTWARE. 53 54-- 55For the MD5 Message-Digest Algorithm: 56 57 Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All rights 58 reserved. 59 60 License to copy and use this software is granted provided that it is 61 identified as the "RSA Data Security, Inc. MD5 Message-Digest Algorithm" in 62 all material mentioning or referencing this software or this function. 63 64 License is also granted to make and use derivative works provided that such 65 works are identified as "derived from the RSA Data Security, Inc. MD5 66 Message-Digest Algorithm" in all material mentioning or referencing the 67 derived work. 68 69 RSA Data Security, Inc. makes no representations concerning either the 70 merchantability of this software or the suitability of this software for 71 any particular purpose. It is provided "as is" without express or implied 72 warranty of any kind. 73 74 These notices must be retained in any copies of any part of this 75 documentation and/or software. 76 77-- 78For MT19937: 79 80 Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura, All 81 rights reserved. 82 83 Redistribution and use in source and binary forms, with or without 84 modification, are permitted provided that the following conditions are 85 met: 86 87 1. Redistributions of source code must retain the above copyright notice, 88 this list of conditions and the following disclaimer. 89 90 2. Redistributions in binary form must reproduce the above copyright 91 notice, this list of conditions and the following disclaimer in the 92 documentation and/or other materials provided with the distribution. 93 94 3. The names of its contributors may not be used to endorse or promote 95 products derived from this software without specific prior written 96 permission. 97 98 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS 99 IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 100 THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 101 PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR 102 CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 103 EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 104 PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 105 PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 106 LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 107 NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 108 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 109 110-- 111For libbacktrace: 112 113 Copyright (C) 2012-2016 Free Software Foundation, Inc. 114 115 Redistribution and use in source and binary forms, with or without 116 modification, are permitted provided that the following conditions are met: 117 118 (1) Redistributions of source code must retain the above copyright 119 notice, this list of conditions and the following disclaimer. 120 121 (2) Redistributions in binary form must reproduce the above copyright 122 notice, this list of conditions and the following disclaimer in 123 the documentation and/or other materials provided with the 124 distribution. 125 126 (3) The name of the author may not be used to endorse or promote 127 products derived from this software without specific prior 128 written permission. 129 130 THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR 131 IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 132 OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN 133 NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 134 SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED 135 TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 136 PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 137 LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 138 NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 139 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 140 141-- 142For SSW Library (align-ssw.C and align-ssw.H): 143 144 The MIT License 145 146 Copyright (c) 2012-2015 Boston College. 147 148 Permission is hereby granted, free of charge, to any person obtaining 149 a copy of this software and associated documentation files (the 150 "Software"), to deal in the Software without restriction, including 151 without limitation the rights to use, copy, modify, merge, publish, 152 distribute, sublicense, and/or sell copies of the Software, and to 153 permit persons to whom the Software is furnished to do so, subject to 154 the following conditions: 155 156 The above copyright notice and this permission notice shall be 157 included in all copies or substantial portions of the Software. 158 159 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 160 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 161 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 162 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS 163 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN 164 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN 165 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 166 SOFTWARE. 167 168 169 The 2-clause BSD License 170 171 Copyright 2006 Michael Farrar. 172 173 Redistribution and use in source and binary forms, with or without 174 modification, are permitted provided that the following conditions are 175 met: 176 177 1. Redistributions of source code must retain the above copyright 178 notice, this list of conditions and the following disclaimer. 179 180 2. Redistributions in binary form must reproduce the above copyright 181 notice, this list of conditions and the following disclaimer in the 182 documentation and/or other materials provided with the distribution. 183 184 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 185 "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 186 LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR 187 A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 188 HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 189 SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 190 LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 191 DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY 192 THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 193 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 194 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 195 196-- 197For parasail: 198 199 Pairwise Sequence Alignment Library (parasail) 200 201 Copyright (c) 2015, Battelle Memorial Institute 202 203 1. Battelle Memorial Institute (hereinafter Battelle) hereby grants 204 permission to any person or entity lawfully obtaining a copy of this 205 software and associated documentation files (hereinafter “the 206 Software”) to redistribute and use the Software in source and binary 207 forms, with or without modification. Such person or entity may use, 208 copy, modify, merge, publish, distribute, sublicense, and/or sell 209 copies of the Software, and may permit others to do so, subject to 210 the following conditions: 211 212 - Redistributions of source code must retain the above copyright 213 notice, this list of conditions and the following disclaimers. 214 215 - Redistributions in binary form must reproduce the above copyright 216 notice, this list of conditions and the following disclaimer in 217 the documentation and/or other materials provided with the 218 distribution. 219 220 - Other than as used herein, neither the name Battelle Memorial 221 Institute or Battelle may be used in any form whatsoever without 222 the express written consent of Battelle. 223 224 - Redistributions of the software in any form, and publications 225 based on work performed using the software should include the 226 following citation as a reference: 227 228 Daily, Jeff. (2016). Parasail: SIMD C library for global, 229 semi-global, and local pairwise sequence alignments. *BMC 230 Bioinformatics*, 17(1), 1-11. doi:10.1186/s12859-016-0930-z 231 232 2. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 233 "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 234 LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 235 FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL BATTELLE 236 OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 237 SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 238 LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF 239 USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 240 ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 241 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT 242 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF 243 SUCH DAMAGE. 244 245