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LICENSE.txt
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=============================================
|| SaGePhy ||
=============================================
-------------------- LICENSE --------------------
SaGePhy is licensed under the New BSD License.
-------------------- DISCLAIMER --------------------
Copyright (c) 2018, Soumya Kundu and Mukul S. Bansal
All rights reserved.
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 <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 <COPYRIGHT HOLDER> 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.
-------------------- CITATION --------------------
"SaGePhy: An improved phylogenetic simulation framework for gene and subgene evolution
Soumya Kundu and Mukul S. Bansal
Available from https://compbio.engr.uconn.edu/software/sagephy/
Manuscript under review."
=============================================
|| JPRIME ||
=============================================
-------------------- LICENSE --------------------
JPrIME is licensed under the New BSD License.
-------------------- DISCLAIMER --------------------
Copyright (c) 2012, Computational Biology groups at SciLifeLab Stockholm.
All rights reserved.
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 SciLifeLab 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 COMPUTATIONAL BIOLOGY GROUPS AT SCILIFELAB STOCKHOLM
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.
-------------------- CITATION --------------------
"JPrIME: Phylogenetics library in Java (version X.X.X).
Available at https://github.com/arvestad/jprime/.
Computational biology groups, Science for Life Laboratory Stockholm."
==============================================
|| BIOJAVA ||
==============================================
-------------------- LICENSE --------------------
BioJava is licensed under GNU LGPL 2.1.
-------------------- CITATION --------------------
"BioJava: an Open-Source Framework for Bioinformatics.
R.C.G. Holland; T. Down; M. Pocock; A. Prlić; D. Huen; K. James; S. Foisy; A. Dräger; A. Yates; M. Heuer; M.J. Schreiber.
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn397."
=============================================
|| FORESTER ||
=============================================
-------------------- LICENSE --------------------
Forester is available under GNU Lesser GPL.
-------------------- DISCLAIMER --------------------
Copyright (C) 2012 Christian M. Zmasek. All rights reserved.
-------------------- CITATION --------------------
Please contact Christian M. Zmasek at http://www.cmzmasek.net/.
=============================================
|| JCOMMANDER ||
=============================================
-------------------- LICENSE --------------------
JCommander is released under the Apache 2.0 license.
-------------------- CITATION --------------------
Please contact Cédric Beust at [email protected].
=============================================
|| UNCOMMONS MATHS ||
=============================================
-------------------- LICENSE --------------------
Uncommons Maths is available under the Apache Software Licence, Version 2.0.
-------------------- CITATION --------------------
Please contact Dan Dyer at http://dandyer.co.uk/.
=============================================
|| EJML ||
=============================================
-------------------- LICENSE --------------------
EJML is available under GNU Lesser GPL.
-------------------- CITATION --------------------
Please contact Peter Abeles at [email protected].
=============================================
|| MDSJ ||
=============================================
-------------------- LICENSE --------------------
MDSJ is available under Creative Commons License "by-nc-sa" 3.0.
-------------------- DISCLAIMER --------------------
The MDSJ Java library ("software") is developed and maintained in the Algorithmics Group, Department
of Computer & Information Science, University of Konstanz, Germany ("author"). Some rights reserved.
The software is provided "AS IS", with no warranty, express or implied, including but not limited to
the implied warranties of merchantability and fitness for a particular use. In no event shall the author
be liable for any damages, direct or indirect, even if advised of the possibility of such damages. If you
do not accept these restrictions, you do not have permission to download or use MDSJ.
-------------------- CITATION --------------------
"Algorithmics Group. MDSJ: Java Library for Multidimensional Scaling (Version 0.2).
Available at http://www.inf.uni-konstanz.de/algo/software/mdsj/.
University of Konstanz, 2009."
=============================================
|| APACHE COMMONS ||
=============================================
------------------- LICENSE --------------------
Apache Commons is available under Apache License Version 2.0
=============================================
|| JFREECHART ||
=============================================
------------------- LICENSE --------------------
JFreeChart is available under GNU Lesser General Public Licence.
=============================================
|| REFLECTIONS ||
=============================================
-------------------- LICENSE --------------------
Reflections is available under "DO WHAT THE FUCK YOU WANT TO PUBLIC LICENSE Version 2, December 2004"
-------------------- DISCLAIMER --------------------
Copyright (C) 2004 Sam Hocevar <[email protected]>
Everyone is permitted to copy and distribute verbatim or modified
copies of this license document, and changing it is allowed as long
as the name is changed.
DO WHAT THE FUCK YOU WANT TO PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. You just DO WHAT THE FUCK YOU WANT TO.
-------------------- CITATION --------------------
Please contact Sam Hocevar at [email protected].
=============================================
|| JSCIENCE ||
=============================================
-------------------- LICENSE --------------------
JScience is available under the JScience BSD Licence.
-------------------- DISCLAIMER --------------------
JScience - Java(TM) Tools and Libraries for the Advancement of Sciences.
Copyright (C) 2006 - JScience (http://jscience.org/)
All rights reserved.
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
and include this license agreemeent.
* 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.
-------------------- CITATION --------------------
Please contact Jean-Marie Dautelle at [email protected].
=============================================
|| JGRAPHT ||
=============================================
-------------------- LICENSE --------------------
JGraphT is available under GNU LGPL 2.1.
-------------------- DISCLAIMER --------------------
Copyright (C) 2012 JGraphT team <[email protected]>.
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.
-------------------- CITATION --------------------
Please contact Barak Naveh or the JGraphT team at [email protected].
=============================================
|| GML PARSER ||
=============================================
-------------------- LICENSE --------------------
The GML parser is available under GNU LGPL.
-------------------- DISCLAIMER --------------------
Copyright (C) 2013 Marcus Raitner & Michael Himsolt.
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.
-------------------- CITATION --------------------
Please contact Marcus Raitner at [email protected] or Michael Himsolt at [email protected].