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) 2012 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/>.PLATFORMS:
Although profillic-hmmer 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-hmmer relies on a number of other libraries. All are open source and are easy to install.
HMMER v3 latest source code: svn checkout https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk hmmer
BOOST (tested with version 1.46.1): http://sourceforge.net/projects/boost/files/boost/1.46.1/
Seqan snapshot svn co http://svn.seqan.de/seqan/trunk seqan-trunk
HMMoC-BFloat-Algebra: http://pedlefsen.github.com/HMMoC-BFloat-Algebra/
prolific: http://galosh.github.com/prolific
See the document INSTALL for more information.
Thank you, Paul
Paul T. Edlefsen November 21, 2012
Additional copyrights apply to the entirety of the package: Copyright (C) 1992-2010 Sean R. Eddy Copyright (C) 2000-2010 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/