Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: mmseqs2
Source: https://github.com/soedinglab/MMseqs2
Comment: The system-wide option of these libraries are much preferred than that in lib/
Files-Excluded:
 lib/gzstream
 lib/zstd
 lib/simde
 lib/xxhash

Files: *
Copyright: 2012 The MMseqs Development Team
License: GPL-3

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

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

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

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

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

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

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

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

Files: cmake/AppendTargetProperty.cmake
Copyright: 2015 Google Inc. All rights reserved.
License: BSD-3-clause

Files: cmake/FindASan.cmake
       cmake/FindMSan.cmake
       cmake/FindTSan.cmake
       cmake/FindUBSan.cmake
Copyright: 2013 Matthew Arsenault
License: Expat

Files: cmake/FindAtomic.cmake
Copyright: 2024 Mario-DL
License: Apache-2.0

Files: lib/base64/*
       lib/libmarv/src/base64.h
Copyright: 2013 William Sherif
License: Zlib
 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.

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

Files: lib/alp/*
Copyright: 2008 John Spouge
License: public_domain
                            PUBLIC DOMAIN NOTICE
               National Center for Biotechnology Information
 .
  This software/database is a "United States Government Work" under the
  terms of the United States Copyright Act.  It was written as part of
  the author's official duties as a United States Government employee and
  thus cannot be copyrighted.  This software/database 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.

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

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

Files: lib/ips4o/ips4o/*
       lib/ips4o/ips4o.hpp
Copyright: 2017, Michael Axtmann <michael.axtmann@kit.edu>
           2017, Daniel Ferizovic <daniel.ferizovic@student.kit.edu>
           2017, Sascha Witt <sascha.witt@kit.edu>
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.
 .
 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.

Files: lib/microtar/*
Copyright: 2017 rxi
License: Expat

Files: lib/nedmalloc/malloc.c.h
Copyright: 2006 Doug Lea
License: public-domain
 This is a version (aka dlmalloc) of malloc/free/realloc written by
 Doug Lea and released to the public domain, as explained at
 http://creativecommons.org/licenses/publicdomain.  Send questions,
 comments, complaints, performance data, etc to dl@cs.oswego.edu

Files: lib/libmarv/src/kseqpp/kseqpp.hpp
Copyright: 2008-2011 Attractive Chaos <attractor@live.co.uk>
License: Expat

Files: lib/fmt/fmt/*
Copyright: 2012 - present, Victor Zverovich
License: Expat

Files: lib/fast_float/*
Copyright: 2021 The fast_float authors
License: Apache-2.0 or Expat

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

Files: debian/*
Copyright: 2019 Shayan Doust <hello@shayandoust.me>
License: GPL-3

Files: debian/missing-sources/userguide/eisvogel.tex
Copyright: 2014-2019 John MacFarlane
           2017-2019 Pascal Wagler
License: BSD-3-clause

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:
 .
 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 copyright holder 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: 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.

License: GPL-3
 On Debian systems you can find the full text of the GNU General Public
 License version 3 at /usr/share/common-licenses/GPL-3.

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: Apache-2.0
 On Debian systems you can find the full text of the Apache License
 Version 2.0 at /usr/share/common-licenses/Apache-2.0.
