Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: MetaEuk
Files-Excluded: lib/mmseqs/lib/gzstream
                lib/mmseqs/lib/ips4o
                lib/mmseqs/lib/nedmalloc
                lib/mmseqs/lib/simde
                lib/mmseqs/lib/xxhash
                lib/mmseqs/lib/zstd

Files: *
Copyright: 2018-2023 Eli Levy Karin <eli.levy.karin@gmail.com> and co-authors
License: GPL-3+

Files: lib/mmseqs/cmake/AppendTargetProperty.cmake
Copyright: 2015 Google Inc.
License: BSD-3-clause-Google

Files: lib/mmseqs/cmake/FindASan.cmake
       lib/mmseqs/cmake/FindUBSan.cmake
Copyright: (c) 2013 Matthew Arsenault
License: MIT

Files: lib/mmseqs/cmake/GetGitRevisionDescription.cmake.in
Copyright: 2009-2010 Iowa State University
License: Boost-License-1.0

Files: lib/mmseqs/cmake/xxdi.pl
Copyright: 2013 Greg Kroah-Hartman <gregkh@linuxfoundation.org>
           2013 Linux Foundation
License: GPL-2

Files: lib/mmseqs/data/resources/krona_prelude.html
Copyright: (c) 2011, Battelle National Biodefense Institute (BNBI)
License: BSD-3-clause-BNBI

Files: lib/mmseqs/src/alignment/DistanceCalculator.h
       lib/mmseqs/src/alignment/StripedSmithWaterman.cpp
       lib/mmseqs/src/alignment/StripedSmithWaterman.h
Copyright: 2012-2015 Boston College
           2015 Michael Farrar
           2015 Mengyao Zhao
           2015 Martin Steinegger
           2011 Andrei Mackenzie
License: Expat

Files: lib/mmseqs/src/commons/A3MReader.*
Copyright: 2013 Andrew Gallant
License: Expat

Files: lib/mmseqs/src/commons/tantan.*
Copyright: 2010 Martin C. Frith
License: GPL-3

Files: lib/mmseqs/src/commons/itoa.h
Copyright: 2014 Milo Yip
License: Expat

Files: lib/mmseqs/src/commons/TranslateNucl.h
Copyright: 2012 National Center for Biotechnology Information
License: public_domain

Files: lib/mmseqs/src/commons/Orf.*
Copyright: 2012 National Center for Biotechnology Information
           2012 Mike DiCuccio
License: public_domain

Files: lib/mmseqs/src/commons/MemoryMapped.*
Copyright: 2013 Stephan Brumme
License: zlib/libpng

Files: lib/mmseqs/src/taxonomy/NcbiTaxonomy.*
Copyright: 2010 Miguel Pignatelli
License: GPL-3

Files: lib/mmseqs/lib/base64/*
Copyright: 2013 William Sherif
License: zlib/libpng

Files: lib/mmseqs/lib/simd/simd.h
Copyright: 2012 Martin Steinegger
License: GPL-3

Files:lib/mmseqs/lib/alp/*
Copyright: 2008 John Spouge
License: public_domain

Files: lib/mmseqs/lib/cacode/*
Copyright: 2008 Michiaki Hamada
License: public_domain

Files: lib/mmseqs/lib/ksw2/*
Copyright: 2018 Dana-Farber Cancer Institute
           2017-2018 Broad Institute Inc.
           2008 2009,2011 Attractive Chaos <attractor@live.co.uk>
License: MIT

Files: lib/mmseqs/lib/microtar/*
Copyright: (c) 2017 rxi
License: MIT

Files: lib/mmseqs/lib/omptl/*
Copyright: 2006-2011 Fokko Beekhof <Fokko.Beekhof@unige.ch>
License: LGPL-2.1+

Files: lib/mmseqs/lib/tinyexpr/*
Copyright: 2015-2018 Lewis van Winkle
License: zlib/libpng

License: GPL-2
 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; version 2.
 .
 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.
 .
 You should have received a copy of the GNU General Public License along
 with this program; if not, write to the Free Software Foundation, Inc.,
 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 .
 On Debian systems you can find the full test of the GNU General Public
 License version 2 at /usr/share/common-licenses/GPL-2.

License: GPL-3+
 This package 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 package 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 program. If not, see <http://www.gnu.org/licenses/>
 .
 On Debian systems, the complete text of the GNU General
 Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".

License: GPL-3
 This package 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; version 3.
 .
 This package 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 program. If not, see <http://www.gnu.org/licenses/>
 .
 On Debian systems, the complete text of the GNU General
 Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".

License: BSD-3-clause-Google
 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 Google Inc. 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.

License: BSD-3-clause-BNBI
 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 the Battelle National Biodefense 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, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 HOLDER 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.

License: MIT
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the
 "Software"), to deal in the Software without restriction, including
 without limitation the rights to use, copy, modify, merge, publish,
 distribute, sublicense, and/or sell copies of the Software, and to
 permit persons to whom the Software is 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 Software.
 .
 THE SOFTWARE IS 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 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.

License: Boost-License-1.0
 Permission is hereby granted, free of charge, to any person or organization
 obtaining a copy of the software and accompanying documentation covered by
 this license (the "Software") to use, reproduce, display, distribute,
 execute, and transmit the Software, and to prepare derivative works of the
 Software, and to permit third-parties to whom the Software is furnished to
 do so, all subject to the following:
 .
 The copyright notices in the Software and this entire statement, including
 the above license grant, this restriction and the following disclaimer,
 must be included in all copies of the Software, in whole or in part, and
 all derivative works of the Software, unless such copies or derivative
 works are solely in the form of machine-executable object code generated by
 a source language processor.
 .
 THE SOFTWARE IS 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, TITLE AND NON-INFRINGEMENT. IN NO EVENT
 SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
 FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.
 .
 The license can be found at <http://www.boost.org/LICENSE_1_0.txt>.

License: public_domain
                      PUBLIC DOMAIN NOTICE
         National Center for Biotechnology Information
 .
 With the exception of certain third-party files summarized below, this
 software is a "United States Government Work" under the terms of the
 United States Copyright Act.  It was written as part of the authors'
 official duties as United States Government employees and thus cannot
 be copyrighted.  This software is freely available to the public for
 use. The National Library of Medicine and the U.S. Government have not
 placed any restriction on its use or reproduction.
 .
 Although all reasonable efforts have been taken to ensure the accuracy
 and reliability of the software and data, the NLM and the U.S.
 Government do not and cannot warrant the performance or results that
 may be obtained by using this software or data. The NLM and the U.S.
 Government disclaim all warranties, express or implied, including
 warranties of performance, merchantability or fitness for any
 particular purpose.
 .
 Please cite the author in any work or product based on this material.

License: zlib/libpng
 This software is provided 'as-is', without any express or implied warranty.
 In no event will the authors be held liable for any damages arising from the
 use of this software.
 .
 Permission is granted to anyone to use this software for any purpose, including
 commercial applications, and to alter it and redistribute it freely, subject to
 the following restrictions:
 .
     1. The origin of this software must not be misrepresented; you must not claim
        that you wrote the original software. If you use this software in a product,
        an acknowledgment in the product documentation would be appreciated but
        is not required.
 .
     2. Altered source versions must be plainly marked as such, and must not be
        misrepresented as being the original software.
 .
     3. This notice may not be removed or altered from any source distribution.

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.
 .
 You should have received a copy of the GNU Lesser General Public
 License along with this library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301,
 USA.

License: Expat
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
 in the Software without restriction, including without limitation the rights
 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 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 Software.
 .
 THE SOFTWARE IS 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 SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.

