Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ABySS Upstream-Contact: Shaun Jackman Source: https://github.com/bcgsc/abyss 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, version 3. . 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, see . . For commercial licensing options, please contact Patrick Rebstein Files: * Copyright: Copyright 2016 British Columbia Cancer Agency Branch License: GPL-3 Files: Layout/* Copyright: Copyright 2012 Shaun Jackman License: GPL-3 Files: lib/bloomfilter/* Copyright: Copyright 2016 Justin Chu License: GPL-3 Files: lib/rolling-hash/* Copyright: Copyright 2016 Hamid Mohamadi License: GPL-3 Files: Common/cholesky.hpp Copyright: Copyright 2005 Gunter Winkler, Konstantin Kutzkow License: LGPL-2.1+ Files: Common/city.cc Common/city.h Copyright: Copyright 2011 Google, Inc. License: Expat Files: dialign/* Copyright: Copyright 2008 Amarendran R. Subramanian License: LGPL-2.1+ License: LGPL-2.1+ On Debian systems, see `/usr/share/common-licenses/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 Street, Fifth Floor, Boston, MA 02110-1301 USA . Amarendran R. Subramanian, hereby disclaims all copyright interest in the DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian. . Amarendran R. Subramanian, 2004-2008 . DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig. . Research work using DIALIGN-TX should cite: . DIALIGN-TX: improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern, Algorithms for Molecular Biology 3:6, 2008 . DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005 Files: FMIndex/bit_array.h Copyright: Copyright 2010 Daisuke Okanohara 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 name of the authors nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. Files: FMIndex/sais.hxx Copyright: Copyright 2010 Yuta Mori License: Expat 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. Files: lib/gtest-*/* Copyright: Copyright 2008 Google Inc. 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 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. 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