Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: beast2 Upstream-Contact: Alexei Drummond , Andrew Rambaut Source: https://github.com/CompEvol/beast2 Files-Excluded: */*.jar Files-Excluded-beastfx: */*.jar html/javascript Comment: Excluding embedded jar files and also the javascript directory, it is not used and includes lots of files with very-long-lines. Files: * Copyright: 2002-2009 Alexei Drummond and Andrew Rambaut License: LGPL-2.1+ Files: beastfx/* Copyright: 2011-2019 JFXtras License: BSD-3-clause Files: beastfx/resources/themes/win7.css Copyright: 2014 Matthias Meidinger License: BSD-2-clause-FreeBSD Files: beastfx/src/* Copyright: 2010 Remco Bouckaert License: LGPL-2+ Files: beastfx/src/beastfx/app/beauti/* Copyright: 2013-2014 Tim Vaughan License: LGPL-2.1+ Files: beastfx/src/beastfx/app/inputeditor/* beastfx/src/beastfx/app/tools/TreeTraceAnalysis.java Copyright: 2012-2015 Tim Vaughan License: GPL-3+ Files: beastfx/src/beastfx/app/tools/LogCombinerDialog.java Copyright: 2002-2010 Alexei Drummond and Andrew Rambaut License: LGPL-2+ Files: beastfx/src/beastfx/app/treeannotator/* Copyright: 2002-2010 Alexei Drummond and Andrew Rambaut License: LGPL-2+ Files: release/* Copyright: 2014-2018 Tobias Fischer License: Expat Files: src/beast/base/* Copyright: 2010 Remco Bouckaert remco@cs.auckland.ac.nz License: LGPL-2+ Files: src/beast/base/evolution/RateStatistic.java src/beast/base/evolution/distance/* src/beast/base/evolution/likelihood/BeagleTreeLikelihood.java src/beast/base/evolution/speciation/* src/beast/base/evolution/tree/* src/beast/base/inference/distribution/* src/beast/base/math/* src/beast/base/util/* test/* Copyright: 2002-2010 Alexei Drummond and Andrew Rambaut License: LGPL-2+ Files: src/beast/base/evolution/operator/kernel/* Copyright: 2002-2018 Alexei Drummond, Andrew Rambaut and Marc Suchard License: LGPL-2+ Files: src/beast/base/evolution/operator/kernel/BactrianSubtreeSlide.java src/beast/base/evolution/substitutionmodel/GeneralSubstitutionModel.java src/beast/base/evolution/tree/ClusterTree.java src/beast/base/evolution/tree/Node.java src/beast/base/evolution/tree/TreeParser.java src/beast/base/util/MersenneTwisterFast.java src/beast/base/util/Randomizer.java Copyright: 2010 Remco Bouckaert remco@cs.auckland.ac.nz License: LGPL-2+ Files: src/beast/pkgmgmt/PackageManager.java Copyright: 2010 Remco Bouckaert remco@cs.auckland.ac.nz 2005 University of Waikato, Hamilton, New Zealand License: LGPL-2+ and GPL-2+ Files: src/beast/base/evolution/substitutionmodel/ColtEigenSystem.java src/beast/base/evolution/substitutionmodel/ComplexColtEigenSystem.java src/beast/base/evolution/substitutionmodel/ComplexSubstitutionModel.java src/beast/base/math/LogTricks.java Copyright: 2002-2018 Alexei Drummond, Andrew Rambaut and Marc Suchard License: LGPL-2+ Files: src/beast/base/inference/Operator.java Copyright: 2011 BEAST2 Core Team License: LGPL-2+ Files: src/beast/base/inference/operator/* src/beast/base/inference/parameter/* Copyright: 2010 Joseph Heled jheled@gmail.com License: LGPL-2+ Files: src/beast/base/inference/operator/JointOperator.java Copyright: 2013-2015 Tim Vaughan License: GPL-3+ Files: src/beast/base/inference/operator/kernel/* Copyright: 2002-2018 Alexei Drummond, Andrew Rambaut and Marc Suchard License: LGPL-2+ Files: src/beast/base/inference/parameter/GeneralParameterList.java test/test/beast/evolution/* Copyright: 2013-2014 Tim Vaughan License: LGPL-2.1+ Files: src/beast/base/math/matrixalgebra/RobustEigenDecomposition.java Copyright: 1999 CERN - European Organization for Nuclear Research. License: Colt_License_Agreement Comment: This file is adapted from Colt and does not hold specific license information. Files: src/beast/base/util/MachineAccuracy.java Copyright: 2010 BEAST II Developer Group License: LGPL-2+ Files: src/org/apache/* Copyright: 2003-2016 The Apache Software Foundation License: Apache-2.0 Files: src/org/json/* Copyright: 2010-2015 The Android Open Source Project License: Apache-2.0 Files: debian/* Copyright: 2011-2012 Andreas Tille 2020-2022 Pierre Gruet License: LGPL-2+ 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, 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 the GNU General Public License for more details. . On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. 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, the complete text of the GNU General Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'. License: Apache-2.0 Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to You under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. . On Debian systems you can find the full text of the Apache 2.0 license at /usr/share/common-licenses/Apache-2.0. 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: LGPL-2+ On Debian systems the full text of the LGPL-2 can be found in /usr/share/common-licenses/LGPL-2 License: LGPL-2.1+ On Debian systems, the complete text of the GNU Lesser General Public License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’. License: Colt_License_Agreement Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. CERN makes no representations about the suitability of this software for any purpose. It is provided "as is" without expressed or implied warranty. 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 ORGANIZATION 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: BSD-2-clause-FreeBSD 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. . 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. . The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of the FreeBSD Project.