License.txt

-----------------------------------------------------------------
                  OpenMS -- Open-Source Mass Spectrometry
-----------------------------------------------------------------
Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
ETH Zurich, and Freie Universitaet Berlin 2002-2021.

This software is released under a three-clause BSD license:
 * 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 any author or any participating
   institution may be used to endorse or promote products
   derived from this software without specific prior written
   permission.
For a full list of authors, refer to the file AUTHORS.
-----------------------------------------------------------------
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 ANY OF THE AUTHORS OR THE
CONTRIBUTING INSTITUTIONS 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 source code of OpenMS is available via our homepage
http://www.OpenMS.de

OpenMS depends on third party libraries which are listed below.
The source code of these libraries is available from their
website or can be obtained via a "contrib" package, which
specifically configures these libraries for OpenMS and is
available on our website.

The respective license files for the contrib libraries
can be found in the "contrib" package root directory or online
(see below).

libSVM
  - URL:
  http://www.csie.ntu.edu.tw/~cjlin/libsvm/
  - License:
  http://www.csie.ntu.edu.tw/~cjlin/libsvm/COPYRIGHT
	
GLPK
  - URL:
  http://www.gnu.org/s/glpk/
  - License:
  http://www.gnu.org/copyleft/gpl.html

Qt5 (open-source version)
  - URL:
  https://www.qt.io/
  - License:
  http://doc.qt.io/qt-5/licensing.html

Xerces-C
  - URL:
  http://xerces.apache.org/xerces-c/index.html
  - License:
  http://www.apache.org/licenses/LICENSE-2.0

Boost (headers)
  - URL:
  http://www.boost.org/
  - License:
  http://www.boost.org/more/license_info.html

ZLib
  - URL:
  http://www.zlib.net
  - License:
  http://www.zlib.net/zlib_license.html
  
BZ2Lib
  - URL:
  http://www.bzip.org/
  - License:
  http://www.bzip.org/1.0.5/bzip2-manual-1.0.5.html

Eigen
 - URL:
 http://eigen.tuxfamily.org/
 - License:
 https://www.mozilla.org/en-US/MPL/2.0/

Geometric Tools (Wildmagic)
 - URL:
 https://www.geometrictools.com/
 - License:
 http://www.boost.org/LICENSE_1_0.txt
 
HDF5
 - URL:
 https://www.hdfgroup.org/solutions/hdf5/
 - License:
 https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/browse/COPYING

SQLite:
 - URL:
 https://www.sqlite.org/
 - License:
 https://www.sqlite.org/copyright.html

KissFFT
 - URL:
 https://sourceforge.net/projects/kissfft/
 - License:
 https://sourceforge.net/p/kissfft/code/ci/default/tree/COPYING

---------------------   Raw file conversion:  ------------------------

RawFileReader (via ThermoRawFileParser)
- URL:
https://github.com/compomics/ThermoRawFileParse
- License:
https://github.com/compomics/ThermoRawFileParser/blob/master/LICENSE

---------------------   Search engines:  ------------------------
 
OMSSA
  - URL:
  ftp://ftp.ncbi.nlm.nih.gov/pub/lewisg/omssa
  - License:
  Public Domain

Percolator:
  - URL:
  http://percolator.ms/
  - License:
  http://www.apache.org/licenses/LICENSE-2.0

X!Tandem:
  - URL and source code:
  http://www.thegpm.org/tandem/
  - License:
  http://www.perlfoundation.org/attachment/legal/artistic-2_0.txt

MyriMatch:
  - URL and source code:
  https://www.ncbi.nlm.nih.gov/pubmed/17269722
  - License:
  http://www.apache.org/licenses/LICENSE-2.0

MSGF+:
  - URL and source code:
  https://github.com/sangtaekim/msgfplus
  - License:
  https://github.com/sangtaekim/msgfplus/blob/master/LICENSE.txt

Fido:
  - URL and source code:
  https://noble.gs.washington.edu/proj/fido/
  - License:
  https://gist.github.com/hendrikweisser/2d10eb8bf1e370e6dfbb

LuciPhOr2:
  - URL and source code:
  http://luciphor2.sourceforge.net/
  - License:
  http://www.apache.org/licenses/LICENSE-2.0

SpectraST:
  - URL and source code:
 https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/
 trans_proteomic_pipeline/src/Search/SpectraST/ 
  - License:
  https://www.gnu.org/licenses/gpl.html
  https://www.gnu.org/copyleft/lesser.html

SIRIUS:
  - URL:
  https://bio.informatik.uni-jena.de/software/sirius/
  - License:
  https://www.gnu.org/licenses/gpl

Comet:
  - URL and source code:
  https://sourceforge.net/projects/comet-ms/
  - License:
  http://www.apache.org/licenses/LICENSE-2.0

Crux:
  - URL and source code:
  http://crux.ms
  - License:
  http://www.apache.org/licenses/LICENSE-2.0

MaRaCluster:
  - URL and source code:
  https://github.com/statisticalbiotechnology/maracluster
  - License
  http://www.apache.org/licenses/LICENSE-2.0.html

---------------------   CMake Modules:  ------------------------

GetGitRevisionDescription and findCppCheck:
  - URL and source code:
  https://github.com/rpavlik/cmake-modules
  - License
  http://www.boost.org/LICENSE_1_0.txt