Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: UGENE
Upstream-Contact:  UniPro <ugene@unipro.ru>,
                   Ivan Efremov <iefremov@unipro.ru>
Source: http://ugene.unipro.ru/downloads/ugene_get_latest_source.html
Files-Excluded: */src/libs_3rdparty/zlib
                */installer/macosx
                */installer/windows

Files: *
Copyright: © 2008-2015 UniPro <ugene@unipro.ru>
License: GPL-2+

Files: src/corelibs/U2Formats/src/ABIFormat.cpp
       src/corelibs/U2Formats/src/SCFFormat.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 <Todd.Miller@courtesan.com>
License: ISC
 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: GPL-2+

Files: src/plugins_3rdparty/umuscle/src/muscle/*
Copyright: © 2004-2011 Robert C. Edgar <muscle@drive5.com>
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 <dtj@cs.ucl.ac.uk>
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: BSD-3-clause
 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: GPL-3+

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 <geuz@geuz.org>
License: GPL-2+
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/src/include/*
       src/plugins_3rdparty/ball/src/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 <timolassmann@gmail.com>
License: GPL-2+

Files: src/libs_3rdparty/sqlite3/src/*
Copyright: The author D. Richard Hipp <drh@hwaci.com> 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-2-clause
 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 <iefremov@unipro.ru>
	   © 2012 Andreas Tille <tille@debian.org>
License: GPL-3+

License: GPL-2+
 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: GPL-3+
 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.
