Copyright (c) 2014-2018, Pacific Biosciences of California, Inc.

All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted (subject to the limitations in the
disclaimer below) provided that the following conditions are met:

 * 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 Pacific Biosciences nor the names of its
   contributors may be used to endorse or promote products derived
   from this software without specific prior written permission.

NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS
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.

See pbdata/MD5Utils.* for the following:
 /*
   Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
rights reserved.

License to copy and use this software is granted provided that it
is identified as the "RSA Data Security, Inc. MD5 Message-Digest
Algorithm" in all material mentioning or referencing this software
or this function.

License is also granted to make and use derivative works provided
that such works are identified as "derived from the RSA Data
Security, Inc. MD5 Message-Digest Algorithm" in all material
mentioning or referencing the derived work.

RSA Data Security, Inc. makes no representations concerning either
the merchantability of this software or the suitability of this
software for any particular purpose. It is provided "as is"
without express or implied warranty of any kind.

These notices must be retained in any copies of any part of this
documentation and/or software.
 */

See alignment/suffixarray/ssort.hpp for the following:
/****************************************************************
Copyright (C) Lucent Technologies 1997
All Rights Reserved

Permission to use, copy, modify, and distribute this software and
its documentation for any purpose and without fee is hereby
granted, provided that the above copyright notice appear in all
copies and that both that the copyright notice and this
permission notice and warranty disclaimer appear in supporting
documentation, and that the name Lucent Technologies or any of
its entities not be used in advertising or publicity pertaining
to distribution of the software without specific, written prior
permission.

LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.
IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES 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.
****************************************************************/

See alignment/algorithms/sorting/qsufsort.cpp for the following:
/* qsufsort.c
   Copyright 1999, N. Jesper Larsson, all rights reserved.

   This file contains an implementation of the algorithm presented in "Faster
   Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
   Sadakane (sada@is.s.u-tokyo.ac.jp).

   This software may be used freely for any purpose. However, when distributed,
   the original source must be clearly stated, and, when the source code is
   distributed, the copyright notice must be retained and any alterations in
   the code must be clearly marked. No warranty is given regarding the quality
   of this software.*/
