Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: UGENE Upstream-Contact: UniPro , Ivan Efremov Source: http://ugene.unipro.ru/downloads/ugene_get_latest_source.html Files-Excluded: src/libs_3rdparty/zlib installer/macosx installer/windows Files: * Copyright: © 2008-2012 UniPro License: GPL2+ Files: src/corelibs/U2Formats/src/ABIFormat.cpp src/corelibs/U2Formats/src/SCFFormat.cpp src/corelibs/U2Formats/src/IOLibUtils.cpp Copyright: © 1994 Medical Research Council. All rights reserved. License: MCR Permission to use, copy, modify and distribute this software and its documentation for any purpose is hereby granted without fee, provided that this copyright and notice appears in all copies. . MRC disclaims all warranties with regard to this software. Files: src/plugins_3rdparty/hmm2/src/hmmer2/sre_string.cpp Copyright: © 1998 Todd C. Miller License: BSD Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. . THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. Files: src/plugins_3rdparty/hmm2/* Copyright: © 1992-2003 HHMI/Washington University School of Medicine License: GPL2+ Files: src/plugins_3rdparty/umuscle/src/muscle Copyright: © 2004-2011 Robert C. Edgar License: PD The software is provided as PUBLIC DOMAIN (see http://www.drive5.com/muscle/license.htm) Files: src/plugins_3rdparty/psipred/src/seq2mtx.cpp src/plugins_3rdparty/psipred/src/sspred_avpred.cpp src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp Copyright: © 2000 D.T. Jones License: non-free_in_clause_8 BY USING THE PROGRAM YOU ARE ACKNOWLEDGING THE FACT THAT YOU AGREE TO THE TERMS OUTLINED IN THIS AGREEMENT. USERS WISHING TO USE THE SOFTWARE FOR COMMERCIAL ACTIVITIES NOT COVERED BY THIS AGREEMENT SHOULD SEND E-MAIL TO: dtj@cs.ucl.ac.uk . * NOTE RECENT CHANGES TO PARAGRAPH 8 * . In regard to the protein structure prediction program (PSIPRED2) herewith (the Software) the copyright and other intellectual property rights to which belong to the Author(s). . Any user (the User) of the program undertakes to the Copyright holder that he or she shall be bound by the following terms and conditions: . 1. The User will receive the Software and any related documentation in confidence and will not use the same except for the purpose of their own research. The Software will be used only by such of the User's officers or employees to whom it must reasonably be communicated to enable them to undertake their research and who agree to be bound by the same confidence. The User shall procure and enforce such agreement from his or her staff for the benefit of the Copyright holder. . 2. The publication of research using the Software must include an appropriate citation to the method: . Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202. . 3. All forms of the Software will be kept in a reasonably secure place to prevent unauthorised access. . 4. Each copy of the Software or, if not practicable then, any package associated therewith shall be suitably marked (and such marking maintained) with the following copyright notice: "Copyright 2000 D.T.Jones. All Rights Reserved.". . 5. The Software may be modified, but any changes made shall be communicated to the Author(s) and made freely available. . 6. The Software may not be sold as a standalone package, or incorporated into a commercial software package without the written permission of the Copyright holder. The Software may be used freely for individual academic or commercial research. The Software may also be made freely available for training or teaching purposes. . 7. The results produced by the Software may not be incorporated into any data banks or databases which are subject to the payment of access or license fees without the written permission of the Copyright holder. . 8. The Software may be made available to users over a local network or wide area network (including the Internet), but only if access is granted free of charge to all authorised users. Incorporation of the Software into a commercial Web site or other fee paying service is not allowed without the written permission of the Copyright holder. If PSIPRED results are returned to the user via such a network service, then a suitable acknowledgement of the PSIPRED method must be returned somewhere in the output text. . 9. The confidentiality obligation in paragraph one shall not apply: . (i) to information and data known to the User at the time of receipt hereunder (as evidenced by its written records); . (ii) to information and data which was at the time of receipt in the public domain or thereafter becomes so through no wrongful act of the User; . (iii) to information and data which the User receives from a third party not in breach of any obligation of confidentiality owed to the Author(s). . 10. The User understands that the Software is supplied "as is". No warranty as to its fitness or suitability for any purpose whatsoever is made or implied. In no event shall the Author(s) or Copyright holder be held responsible for any direct or indirect damages arising through the use of the Software. Files: src/plugins_3rdparty/primer3/src/primer3_core Copyright: © 1996-2007 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), and Helen Skaletsky License: BSDlike Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the names of the copyright holders nor contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: src/plugins_3rdparty/hmm3/src/hmmer3/* Copyright: © 2000-2009 Howard Hughes Medical Institute (and others) License: GPL3+ Files: src/plugins_3rdparty/hmm3/src/hmmer3/easel/* Copyright: © 2006-2009 Howard Hughes Medical Institute (and others) License: JaneliaFarm Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. Neither the name of the Howard Hughes Medical Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: src/plugins/biostruct3d_view/src/gl2ps Copyright: © 1999-2006 Christophe Geuzaine License: GPL2+ Note: Alternatively you can choose the GL2PS License as published by Christophe Geuzaine, either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See either the GNU Library General Public License or the GL2PS License for more details. Comment: Debian just contains this code in libgl2ps-dev Files: src/plugins_3rdparty/ball/include/* src/plugins_3rdparty/ball/source/* Copyright: © 1996-2012 Oliver Kohlbacher, Hans-Peter Lenhof, Andreas Hildebrandt License: LGPL-2.1 This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . On Debian systems, see /usr/share/common-licenses/LGPL-2.1 for the full text of the license. Files: src/plugins_3rdparty/phylyp/src Copyright: © 1993-2004 by the University of Washington. Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. License: non-free_phylip Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed. Files: src/plugins_3rdparty/kalign/src Copyright: © 2006 Timo Lassmann License: GPL2+ Files: src/libs_3rdparty/sqlite3/src Copyright: The author D. Richard Hipp disclaims copyright to this source code. License: PD+blessing In place of a legal notice, here is a blessing: . May you do good and not evil. May you find forgiveness for yourself and forgive others. May you share freely, never taking more than you give. Files: src/include/opencl/legacy/* Copyright: © 2008-2010 The Khronos Group Inc. License: BSD+Khronos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and/or associated documentation files (the "Materials"), to deal in the Materials without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Materials, and to permit persons to whom the Materials are furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Materials. . THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS. Files: src/corelibs/U2Private/src/StackWalker.* Copyright: © 2005-2011 Jochen Kalmbach License: BSD-like Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of Jochen Kalmbach nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: debian/* Copyright: © 2008-2011 Ivan Efremov © 2012 Andreas Tille License: GPL3+ License: GPL2+ This suite of programs is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . In other words, you are free to modify, copy, or redistribute this source code and its documentation in any way you like, but you must distribute all derivative versions as free software under the same terms that I've provided my code to you (i.e. the GNU General Public License). This precludes any use of the code in proprietary or commercial software unless your source code is made freely available. . If you wish to use Unipro UGENE code under a different Open Source license that's not compatible with the GPL (like the Artistic License, BSD license, or the Netscape Public License), please contact us (ugene@unipro.ru) for permission. . Incorporation into commercial software under non-GPL terms is possible by obtaining a specially licensed version from Unipro. Contact 'ugene@unipro.ru' to arrange licensing terms. . This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this Unipro UGENE release, in the file LICENSE; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. . On Debian systems, see /usr/share/common-licenses/GPL-2 for the complete text of the GPL. License: GPL3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . On Debian systems, see /usr/share/common-licenses/GPL-3 for the complete text of the GPL.