This is profillic-hmmer, modified versions of HMMER 3 programs to
implement interoperability with galosh profiles (as generated by
profillic).  Please see the document CITING, which should have been
included with this file.  You may use at will, subject to the license
(GPL v3), but *please cite the relevant papers* in your
documentation and publications associated with uses of this library.
Thank you!

Copyright (C) 2011 by Paul T Edlefsen, Fred Hutchinson Cancer Research
Center.

AND see the original copyright notice for HMMER3, reproduced below (as this is a derivative work only very slightly modifying their code and depending on HMMER3 entirely).

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program 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 program.  If not, see <http://www.gnu.org/licenses/>.

icensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

-----
PLATFORMS:

Although profillic has been designed for cross-platform use, the
current version has only been tested on Mac OS X systems.  It should
easily install on any other *nix platform.  If you are on Windows, and
want to compile this, we recommend using Cygwin.  If you are able to
compile this on Windows or elsewhere, please let us know and tell us
what you did to make it happen.  Thanks.

DEPENDENCIES:

profillic relies on a number of other libraries.  All are open source
and are easy to install.

Required external libraries:
---
HMMER v3.0 source code (exactly v3.0; later versions will probably not work):
ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz

BOOST (tested with version 1.46.1):
http://sourceforge.net/projects/boost/files/boost/1.46.1/

Seqan version 1.2 (Note that the most recent version is 1.3 but we
have not yet updated our code to be compatible with the new version,
so you'll have to get version 1.2):
http://www.seqan.de/uploads/media/Seqan_Release_1.2.zip

HMMoC-BFloat-Algebra:
http://pedlefsen.github.com/HMMoC-BFloat-Algebra/

Required galosh libraries:
---
prolific:  http://galosh.github.com/prolific

See the document INSTALL for more information.

Thank you,
  Paul

Paul T. Edlefsen
July 10, 2011

====================== HMMER 3 COPYRIGHT =========================
HMMER - Biological sequence analysis with profile hidden Markov models
Copyright (C) 2010 Howard Hughes Medical Institute.
------------------------------------------------------------------

Additional copyrights apply to the entirety of the package:
Copyright (C) 1992-2009 Sean R. Eddy
Copyright (C) 2000-2009 Howard Hughes Medical Institute
Copyright (C) 1992-2004 Washington University School of Medicine
Copyright (C) 1992-1994 MRC Laboratory of Molecular Biology

The code includes contributions and input from the members of the
HMMER development team and the Eddy/Rivas laboratories at HHMI Janelia
Farm, whose current members include:

   Sean Eddy          Janelia Farm 
   Sergi Castellano   Janelia Farm 
   Goran Ceric        Janelia Farm
   Michael Farrar     Janelia Farm 
   Rob Finn           Wellcome Trust Sanger Institute
   Bjarne Knudsen     CLC bio
   Diana Kolbe        Washington University/Janelia Farm
   Eric Nawrocki      Janelia Farm
   Elena Rivas        Janelia Farm
   Travis Wheeler     Janelia Farm

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

   Jeremy Buhler                   Washington University
   Ian Holmes                      UC Berkeley
   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 has its own license and
copyright information. See easel/COPYRIGHT and easel/LICENSE.

HMMER includes patent-pending SIMD technology under nonexclusive
license from Michael Farrar. You are sublicensed to use this
technology specifically for the use, modification, and redistribution
of HMMER3, under the terms of the GPLv3 patent clause.

This source code is distributed under the terms of the GNU General
Public License. See the file LICENSE for details.

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at
your option) any later version.

This program 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.

A copy of the GNU General Public License is in the file LICENSE.  You
may also obtain a copy from <http://www.gnu.org/licenses/>.

"HMMER" is a trademark of the Howard Hughes Medical Institute.
Although the code is freely available as open source, we intend that
only the version at http://hmmer.org/ is known as HMMER. You are free
to create a modified version and distribute it (subject to the terms
of the GPL), but we ask that you name it something that would not be
confused with HMMER itself.

------------------------------------------------------------------
The HMMER development team
HHMI Janelia Farm Research Campus
http://hmmer.org/