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.