Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: EMBOSS core development team Source: ftp://emboss.open-bio.org/pub/EMBOSS/ Files: * Copyright: The EMBOSS developers or their employers. License: emboss EMBOSS License (http://emboss.sourceforge.net/licence/) . The AJAX and NUCLEUS libraries are released under the GNU Lesser General Public Licence. . The EMBOSS Administrator’s Guide can be copied, distributed and/or modified under the terms of the GNU Free Documentation License, Version 1.1 or any later version published by the Free Software Foundation; with no Invariant Sections, with no Front-Cover Texts, and with no Back-Cover Texts. A copy of the license is included in the chapter entitled ”GNU Free Documentation License”. . The EMBOSS Quick Guide has been relicenced and can be used, modified and distributed under the same terms as EMBOSS itself. . EMBOSS applications are released under the GNU General Public Licence. . Parsing of ACD files does not constitute a "derived work" and developers are encouraged to do this, for example to write their own GUIs. . For developers who have their own licensing conditions already in effect, there will be an additional way to contribute. The EMBASSY collection can include packages that use the EMBOSS core libraries and interfaces but under their own licensing conditions. They will be bound by the Library GPL of the AJAX and NUCLEUS libraries, but not necessarily by the full GPL. . Some of the suggestions and code examples from David Hanson's book "C Interfaces and Implementations" are included in the AJAX library. This library is available from http://www.cs.princeton.edu/software/cii/ or ftp://ftp.cs.princeton.edu/pub/packages/cii/ . The COPYRIGHT file in release 1.10 says: . > The author of this software is David R. Hanson. > > Copyright (c) 1994,1995,1996 by David R. Hanson. All Rights Reserved. > > Permission to use, copy, modify, and distribute this software for any > purpose, subject to the provisions described below, without fee is > hereby granted, provided that this entire notice is included in all > copies of any software that is or includes a copy or modification of > this software and in all copies of the supporting documentation for > such software. > > THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED > WARRANTY. IN PARTICULAR, THE AUTHOR DOES MAKE ANY REPRESENTATION OR > WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR > ITS FITNESS FOR ANY PARTICULAR PURPOSE. > > David Hanson / drh@cs.princeton.edu / http://www.cs.princeton.edu/~drh/ > Wed Apr 24 13:44:16 PDT 1996 > Mon Dec 12 15:58:13 EST 1994 Comment: On Debian systems, the complete text of the GNU General Public License version 2, the GNU Free Documentation License version 1.2, and the GNU Library General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’, ‘/usr/share/common-licenses/GFDL-1.2’ and ‘/usr/share/common-licenses/LGPL-2’ respectively. Files: ajax/pcre/* Copyright: © 1997-2000 University of Cambridge License: PCRE_license PCRE is a library of functions to support regular expressions whose syntax and semantics are as close as possible to those of the Perl 5 language. . Written by: Philip Hazel . University of Cambridge Computing Service, Cambridge, England. Phone: +44 1223 334714. . Copyright (c) 1997-2000 University of Cambridge . Permission is granted to anyone to use this software for any purpose on any computer system, and to redistribute it freely, subject to the following restrictions: . 1. This software 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. . 2. The origin of this software must not be misrepresented, either by explicit claim or by omission. In practice, this means that if you use PCRE in software which you distribute to others, commercially or otherwise, you must put a sentence like this . Regular expression support is provided by the PCRE library package, which is open source software, written by Philip Hazel, and copyright by the University of Cambridge, England. . somewhere reasonably visible in your documentation and in any relevant files or online help data or similar. A reference to the ftp site for the source, that is, to . ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/ . should also be given in the documentation. . 3. Altered versions must be plainly marked as such, and must not be misrepresented as being the original software. . 4. If PCRE is embedded in any software that is released under the GNU General Purpose Licence (GPL), then the terms of that licence shall supersede any condition above with which it is incompatible. Files: plplot/* Copyright: © 1987, 1988 by Digital Equipment Corporation, Maynard, Massachusetts, © 1991, 1993, 1994 Wesley Ebisuzaki © 1992, 1993, 1994, 1995, 2001, 2002, 2004 Maurice LeBrun © 1992, 1999, 2001 Geoffrey Furnish © 1992, Maurice J. LeBrun, Geoff Furnish, Tony Richardson. © 2000, 2001, 2002, 2004, 2005 Alan W. Irwin © 2000, 2001, 2002, 2003, 2004 Joao Cardoso © 2001, 2003, 2004, 2005 Rafael Laboissiere © 2001, 2002, 2003, 2004 Andrew Roach © 2002, Vincent Darley © 2004, 2005 Thomas J. Duck © 2004, 2005, 2006 Andrew Ross © 2006, Hazen Babcock © 2006, Jim Dishaw © 2006, Werner Smekal License: GPL-2+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 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 Library General Public License for more details. . On Debian systems you can find a copy of the GNU Library General Public License version 2 at /usr/share/common-licenses/LGPL-2. Files: ajax/zlib/* Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler License: zlib This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. . Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu Files: doc/programs/html/antigenic.html doc/programs/html/pasteseq.html doc/programs/html/showpep.html doc/programs/master/emboss/apps/inc/acdc.input doc/programs/master/emboss/apps/inc/acdtrace.input doc/programs/master/emboss/apps/inc/antigenic.input doc/programs/master/emboss/apps/inc/pasteseq.input doc/programs/master/emboss/apps/inc/showpep.input doc/programs/text/antigenic.txt doc/programs/text/pasteseq.txt doc/programs/text/showpep.txt test/data/amir.swiss test/data/uniprotft.sw test/swiss/seq.dat test/swnew/trembl.dat Copyright: none These files are marked to be copyrighted by the UniProt Consortium, but this applies to the UniProt database as a whole, not to the individual records. License: not-the-CC-BY-ND-3.0 Despite the following statement: . Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms Distributed under the Creative Commons Attribution-NoDerivs License . The above files, as individual records, are not copyrighted. The statement is for the UniProt as a whole. Files: ajax/core/ajvarbcf.c Copyright: © 2010 Broad Institute © The EMBOSS developers License: LGPL-2.1+ and MIT Files: emboss/data/TAXONOMY/*.dmp Homepage: http://www.ncbi.nlm.nih.gov/taxonomy Copyright: Probably public domain (under investigation). License: CC-BY-3.0 Files: emboss/data/OBO/*.obo Homepage: https://github.com/oborel/obo-relations Copyright: 2008-2013 Chris Mungall et all License: CC-BY-3.0 Comment: see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=694908 Files: emboss/data/OBO/chebi.obo Homepage: http://www.ebi.ac.uk/chebi/ Copyright: Public domain according to answer or authors available at https://lists.debian.org/debian-med/2013/01/msg00012.html License: CC-BY-3.0 Files: emboss/data/OBO/software.obo Homepage: http://theswo.sourceforge.net/ Copyright: 2011-2012 James Malone Comment: The statement of the author can be seen at http://bugs.debian.org/694908#92 as long as the license is not yet published on its homepage License: Apache-2.0 On Debian systems you can find the complete text of the Apache License Version 2.0 at /usr/share/common-licenses/Apache-2.0. Files: emboss/data/OBO/pathway.obo Homepage: http://www.obofoundry.org/cgi-bin/detail.cgi?id=pathway Source: ftp://rgd.mcw.edu/pub/data_release/ Copyright: 2009-2012 Victoria Petri License: CC-BY-3.0 Comment: See ftp://rgd.mcw.edu/pub/data_release/PathwayOntology_introduction.doc Files: emboss/data/OBO/eco.obo Homepage: https://github.com/evidenceontology/evidenceontology Copyright: 2009-2013 Marcus Chibucos , Michelle Giglio License: GPL-3+ Files: emboss/data/OBO/ro.obo Homepage: https://github.com/oborel/obo-relations Copyright: 2009-2013 Chris Mungall and others License: CC-BY-3.0 Files: emboss/data/OBO/so.obo Homepage: http://www.sequenceontology.org/ Copyright: 2009-2013 Sequence Ontology Karen Eilbeck License: PD The Sequence Ontology is in the public domain. It is available to public and private sector users with no licensing requirements. We ask that you cite SO and do not make changes to SO then redistribute under the same name. . See http://www.sequenceontology.org/resources/faq.html#lic Files: debian/* Copyright: 2002-2004 Matt Hope 2007-2013 Charles Plessy 2012-2013 Andreas Tille License: LGPL-2.1+ Comment: The EMBOSS package for Debian was initially prepared by Matt Hope (dopey@debian.org) in 2002-2004 and released on (http://debian.bioinformatics.unsw.edu.au/). The package distributed in Debian was prepared by the "pkg-emboss" project in 2006, using the work of Matt Hope as a starting point. Feel free to use the work of the pkg-emboss project as if it were in the public domain. The license of the packaging (LGPL-2.1+) was chosen in 2013 to be as close as possible to upstream's licenses (LGPL-2.1+ for the libraries, GPL-2+ for the applications, and GFDL-NIV-1.1 for some of the documentation). After applyint patches, please be kind to submit them to Upstream under terms that are convenient for them. License: CC-BY-3.0 Attribution 3.0 Unported . 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