HMMER - Biological sequence analysis with profile hidden Markov models

Copyright (C) 1992-2016 Sean R. Eddy
Copyright (C) 2000-2016 Howard Hughes Medical Institute
Copyright (C) 2015-2016 President and Fellows of Harvard College
Copyright (C) 1992-2006 Washington University School of Medicine
Copyright (C) 1992-1994 MRC Laboratory of Molecular Biology

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HMMER is open source software, freely distributed under the terms of a
standard BSD (Berkeley Software Distribution) license:

   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 copyright holder 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 HOLDER 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.

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HMMER's code includes contributions from the members of the HMMER
development team and the Eddy/Rivas laboratories at Harvard
University, whose current and past members include:

   Sean Eddy            HHMI | Harvard University
   Sergi Castellano     Max Planck Leipzig, Germany
   Goran Ceric          HHMI Janelia Research Campus
   Alex Coventry        Cornell University
   Michael Farrar       deceased, 2010
   Rob Finn             European Bioinformatics Institute (EBI)
   Steve Johnson        Monsanto 
   Diana Kolbe          University of Iowa
   Eric Nawrocki        National Center for Biotechnology Information (NCBI)
   Elena Rivas          Harvard University
   Travis Wheeler       University of Montana

HMMER also includes contributions from others, including copyrighted
and licensed code and technology. These are noted in the appropriate
places in source files. These include:

   Jeremy Buhler                   Washington University
   Ian Holmes                      UC Berkeley
   Bjarne Knudsen                  CLC bio, Aarhus Denmark
   Erik Lindahl                    Stanford University
   Graeme Mitchison                Cambridge University
   Lee Newberg                     Rensselaer Polytechnic Institute

   Apple Computer                  Cupertino, CA
   Free Software Foundation, Inc.  Cambridge, MA
   IBM TJ Watson Research Center   Yorktown Heights, NY
   X Consortium                    Cambridge, MA
   
HMMER uses the Easel software library, which is also open source and
BSD licensed. See lib/easel/LICENSE.

HMMER includes patent-pending SIMD technology provided under
nonexclusive license from Michael Farrar (USPTO application
11/696,338, 2008). You are sublicensed to use this technology
specifically for the use, modification, and redistribution of HMMER
source code.

"HMMER" is a trademark of the Howard Hughes Medical Institute.

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Sean Eddy
HHMI | Harvard University
http://hmmer.org/
