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third_party_software_notice.txt
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third_party_software_notice.txt
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Third Party Software Licenses/Notices
This document contains third party software notices and/or additional terms and conditions for licensed third party software components included within Karp.
1) kallisto v.043.0
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Copyright ©2015. The Regents of the University of California (Regents). All Rights Reserved. Permission to use, copy, modify, and distribute this software and its documentation for educational and research not-for-profit purposes, without fee and without a signed licensing agreement, is hereby granted, provided that the above copyright notice, this paragraph and the following two paragraphs appear in all copies, modifications, and distributions. Contact The Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite 510, Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing opportunities.
Created by Nicolas Bray, Harold Pimentel, Pall Melsted and Lior Pachter, University of California, Berkeley
IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
2) SSW Library: An SIMD Smith-Waterman C/C++/Python/Java Library for Use in Genomic Applications – rev. 6/29/16
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Copyright (c) 2012-2015 Boston College
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.
3) Templatized C++ Command Line Parser Library
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Copyright (c) 2003 Michael E. Smoot
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.
4) Eigen Library
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Eigen is primarily MPL2 licensed. See karpeigen/COPYING.MPL2 and
http://www.mozilla.org/MPL/2.0/
http://www.mozilla.org/MPL/2.0/FAQ.html
Some files contain third-party code under BSD or LGPL licenses.
All the LGPL code is either LGPL 2.1-only, or LGPL 2.1-or-later.
For this reason, the COPYING.LGPL file contains the LGPL 2.1 text.
For full details see karpeigen/COPYING.*