Emboss

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Emboss

http://emboss.sourceforge.net
european molecular biology open software suite

EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true free software spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.


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Licensing

LicenseVerified byVerified onNotes
ZlibDebian20 March 2013
License: zlib

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
OtherDebian20 March 2013
License: not-the-CC-BY-ND-3.0

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.
OtherDebian20 March 2013
License: unclear

unclear 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. The packaging work of the pkg-emboss project is in the public domain

unless stated otherwise.
OtherDebian20 March 2013
License: emboss

emboss EMBOSS License (http://emboss.sourceforge.net/licence/)

The AJAX and NUCLEUS libraries are released under the GNU Library 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
OtherDebian20 March 2013
License: PCRE

PCRE 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 <ph10@cam.ac.uk>

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.
License:GPLv2orlaterDebian20 March 2013
License: GPL-2+

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.

You should have received a copy of the GNU Library General Public License along with this library; if not, write to the Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA

02110-1301 USA



Leaders and contributors

Resources and communication

AudienceResource typeURI
Downloadftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz


Software prerequisites



Entry



Date 2013-03-20
Source Debian import
Source link http://packages.debian.org/sid/emboss

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Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.

The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.