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: *
Copyright: 2002-2011 Alexei Drummond, Andrew Rambaut, and Walter Xie
License: LGPL-2.1+

Files: release/Mac/stub/*
Copyright: 2014-2021 Tobias Fischer
License: Expat

Files: src/beast/app/tools/LogCombinerDialog.java
       src/beast/app/treeannotator/TreeAnnotator.java
       src/beast/app/treeannotator/TreeAnnotatorDialog.java
       src/beast/evolution/alignment/distance/*
       src/beast/evolution/branchratemodel/*
       src/beast/evolution/likelihood/BeagleTreeLikelihood.java
       src/beast/evolution/speciation/*
       src/beast/evolution/tree/*
       src/beast/math/*
       src/beast/util/FrequencySet.java
       src/test/beast/beast2vs1/*
Copyright: 2002-2010 Alexei Drummond and Andrew Rambaut
License: LGPL-2+

Files: src/beast/evolution/operators/JointOperator.java
       src/beast/evolution/tree/TreeTraceAnalysis.java
       src/beast/app/draw/IntegerListInputEditor.java
       src/test/beast/evolution/tree/RandomTreeTest.java
Copyright: 2012-2015 Tim Vaughan
License: GPL-3+

Files: src/beast/core/parameter/GeneralParameterList.java
       src/beast/app/beauti/JPackageRepositoryDialog.java
Copyright: 2013-2014 Tim Vaughan
License: LGPL-2.1+

Files: src/beast/evolution/alignment/Sequence.java
       src/beast/evolution/alignment/Alignment.java
       src/beast/evolution/likelihood/TreeLikelihood.java
       src/beast/evolution/likelihood/ThreadedTreeLikelihood.java
       src/beast/evolution/likelihood/ThreadedLikelihoodCore.java
       src/beast/evolution/likelihood/LikelihoodCore.java
       src/beast/evolution/operators/Exchange.java
       src/beast/evolution/operators/TreeOperator.java
       src/beast/evolution/operators/SubtreeSlide.java
       src/beast/evolution/operators/Uniform.java
       src/beast/evolution/operators/WilsonBalding.java
       src/beast/evolution/operators/ScaleOperator.java
       src/beast/evolution/tree/Node.java
       src/beast/evolution/sitemodel/SiteModel.java
       src/beast/evolution/substitutionmodel/Frequencies.java
       src/beast/evolution/substitutionmodel/TN93.java
       src/beast/evolution/substitutionmodel/GeneralSubstitutionModel.java
       src/beast/evolution/substitutionmodel/SubstitutionModel.java
       src/beast/evolution/substitutionmodel/HKY.java
       src/beast/util/MersenneTwisterFast.java
       src/beast/util/PackageManager.java
       src/beast/util/XMLParserException.java
       src/beast/util/JSONParserException.java
       src/beast/util/XMLProducer.java
       src/beast/util/ClusterTree.java
       src/beast/util/TreeParser.java
       src/beast/util/JSONParser.java
       src/beast/util/XMLParser.java
       src/beast/util/PackageDependency.java
       src/beast/util/Randomizer.java
       src/beast/core/Distribution.java
       src/beast/core/Input.java
       src/beast/core/Description.java
       src/beast/core/BEASTObject.java
       src/beast/core/State.java
       src/beast/core/util/CompoundDistribution.java
       src/beast/core/MCMC.java
       src/beast/core/Citation.java
       src/beast/core/BEASTInterface.java
       src/beast/core/Logger.java
       src/beast/app/BeastMCMC.java
       src/beast/app/DocMaker.java
       src/beast/app/ModelBuilder.java
       src/beast/app/draw/Document.java
       src/beast/app/draw/InputShape.java
       src/beast/app/draw/Selection.java
       src/beast/app/draw/HelpBrowser.java
       src/beast/app/draw/Arrow.java
       src/beast/app/draw/Shape.java
       src/beast/app/draw/ModelBuilder.java
       src/beast/app/draw/BEASTObjectShape.java
       src/beast/app/draw/TrackPoint.java
Copyright: 2010 Remco Bouckaert <remco@cs.auckland.ac.nz>
License: LGPL-2+

Files: src/beast/app/treeannotator/TreeSetParser.java
Copyright: 2011 Remco Bouckaert <remco@cs.auckland.ac.nz>
License: GPL-2+

Files: src/beast/app/treeannotator/RealNumberField.java
Copyright: 2009 JAM Development Team
License: LGPL-2.1+

Files: src/beast/core/Operator.java
Copyright: 2011 BEAST2 Core Team
License: LGPL-2+

Files: src/beast/core/parameter/BooleanParameter.java
       src/beast/evolution/operators/BitFlipOperator.java
Copyright: 2010 Joseph Heled jheled@gmail.com
License: LGPL-2+

Files: src/beast/math/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>
           2022-2022 Pierre Gruet <pgt@debian.org>
License: LGPL-3+

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 2 can be found in `/usr/share/common-licenses/GPL-3'.

License: LGPL-3+
 This program 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 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.
 .
 You should have received a copy of the GNU Lesser General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 .
 On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included
 in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license
 version 3 is included in the file ‘/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’.
