Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: beast2
Upstream-Contact: Alexei Drummond <alexei@cs.auckland.ac.nz>,
                  Andrew Rambaut <a.rambaut@ed.ac.uk>
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 <remco@cs.auckland.ac.nz>
License: LGPL-2+

Files: beastfx/src/beastfx/app/beauti/*
Copyright: 2013-2014 Tim Vaughan <tgvaughan@gmail.com>
License: LGPL-2.1+

Files: beastfx/src/beastfx/app/inputeditor/*
       beastfx/src/beastfx/app/tools/TreeTraceAnalysis.java
Copyright: 2012-2015 Tim Vaughan <tgvaughan@gmail.com>
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 <tgvaughan@gmail.com>
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 <tgvaughan@gmail.com>
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 <tille@debian.org>
           2020-2022 Pierre Gruet <pgt@debian.org>
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.
