Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Contact: Steven Weaver <sweaver@ucsd.edu>
Upstream-Name: HyPhy
Source: https://github.com/veg/hyphy/releases
Files-Excluded: */SQLite*
                .gitignore
                */.DS_Store

Files: *
Copyright: 1997-2015 Sergei L Kosakovsky Pond <spond@ucsd.edu>
                     Simon D. W. Frost,
                     Spencer V. Muse <muse@stat.ncsu.edu>
                     and others
License: MIT

Files: src/new/bgm.cpp
       src/new/include/bayesgraph.h
Copyright: Copyright (C) 1997-2006 Sergei L Kosakovsky Pond <sergeilkp@mac.com>
                                   Spencer V Muse <muse@stat.ncsu.edu>
                                   Simon DW Frost <sdfrost@ucsd.edu>
                                   Art FY Poon    <apoon@biomail.ucsd.edu>
License: GPL-2+ with runtime exception

Files: src/contrib/mersenne_twister.cpp
       src/contrib/mersenne_twister.h
Copyright: 1997-2002 Makoto Matsumoto and Takuji Nishimura
License: permissive
 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. The names of its contributors may not 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.

Files: src/contrib/gnuregex.h
       src/contrib/regex.cpp
Copyright: 1985-1993 Free Software Foundation, Inc.
License: GPL-2+

Files: debian/*
Copyright: © 2015 Andreas Tille <tille@debian.org>
License: MIT

License: MIT
 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.
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 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.

License: GPL-2+ with runtime exception
 The Debian packaging is licensed under the GPL-2 or any later version,
 see `/usr/share/common-licenses/GPL-2'

License: GPL-2+
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as
 published by the Free Software Foundation.
 .
 This package 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 General Public License for more details.
 .
 You should have received a copy of the GNU General Public License
 along with this package; if not, write to the Free Software
 Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
 .
 On Debian systems, the complete text of the GNU General Public License
 version 2 can be found in `/usr/share/common-licenses/GPL-2'.
