annotate LICENSE.txt @ 7:8d676bbd1f2d

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===============================================================================

		CoreBio Weblogo and Codonlogo : Copyrights and Licenses

===============================================================================

This package is distributed under the new BSD Open Source License. Much 
of the code was written by Gavin E. Crooks, Gary Hon, Steven Brenner, John-Marc
Chandonia, Liana Lareau, David Ding, Clare Gollnick,David Murphy and other contributers.



Copyright Notice 
================
Copyright (c) 2006, The Regents of the University of California, through
Lawrence Berkeley National Laboratory (subject to receipt of any required 
approvals from the U.S. Dept. of Energy).  All rights reserved.

Parts of this software package are covered by the individual copyrights of the
contributers. Please refer to individual source code files for further details.

NOTICE.  This software was developed under funding from the U.S. Department of 
Energy.  As such, the U.S. Government has been granted for itself and others 
acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in 
the Software to reproduce, prepare derivative works, and perform publicly and 
display publicly.  Beginning five (5) years after the date permission to assert 
copyright is obtained from the U.S. Department of Energy, and subject to any 
subsequent five (5) year renewals, the U.S. Government is granted for itself 
and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide 
license in the Software to reproduce, prepare derivative works, distribute 
copies to the public, perform publicly and display publicly, and to permit 
others to do so.


The new BSD Open Source License 
===============================

#  Copyright (c) 2006, The Regents of the University of California, through 
#  Lawrence Berkeley National Laboratory (subject to receipt of any required
#  approvals from the U.S. Dept. of Energy).  All rights reserved.

#  This software is distributed under the new BSD Open Source License.
#  <http://www.opensource.org/licenses/bsd-license.html>
#
#  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 University of California, Lawrence Berkeley 
#  National Laboratory, U.S. Dept. of Energy 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 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 MIT Open Source License 
===========================

Parts of the code are covered by the MIT license, which is equivalent to the
BSD license apart from the third, no promotion clause. Please refer to
individual source code files for further details.

#  Copyright (c) 2003-2004 The Regents of the University of California.
#  Copyright (c) 2005 Gavin E. Crooks
#  Copyright (c) 2006 David Ding
#  Copyright (c) 2006 Clare Gollnick
#  Copyright (c) 2002-2005 ActiveState Corp.

#  This software is distributed under the MIT Open Source License.
#  <http://www.opensource.org/licenses/mit-license.html>
#
#  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.



The Biopython License (biopython.org)
=====================================
Parts of the code are covered by the biopython license, which is functionally
equivalent to the BSD license.

   
#                Biopython License Agreement
# 
# Permission to use, copy, modify, and distribute this software and its
# documentation with or without modifications and for any purpose and
# without fee is hereby granted, provided that any copyright notices
# appear in all copies and that both those copyright notices and this
# permission notice appear in supporting documentation, and that the
# names of the contributors or copyright holders not be used in
# advertising or publicity pertaining to distribution of the software
# without specific prior permission.

# THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
# CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
# OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
# OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
# OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
# OR PERFORMANCE OF THIS SOFTWARE.