Initial commit after foobaring things for good with the old repository

Makefile

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+MAKE = make
+
+CONTRIB = contrib
+PYDIR   = idepi
+SUBDIRS = $(wildcard $(CONTRIB)/hmmer*)
+
+all:
+	@$(foreach var, $(SUBDIRS), make -C $(var) all;)
+
+clean:
+	@-$(foreach var, $(SUBDIRS), make -C $(var) clean;)
+	@-rm $(PYDIR)/*.pyc
+
+distclean: clean
+	@-$(foreach var, $(SUBDIRS), make -C $(var) distclean;)
+	@-rm $(PYDIR)/*.pyc

NOTICE

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+idepi :: (IDentify EPItope) python libraries containing some useful machine
+learning interfaces for regression and discrete analysis (including
+cross-validation, grid-search, and maximum-relevance/mRMR feature selection)
+and utilities to help identify neutralizing antibody epitopes via machine
+learning.
+
+Copyright (C) 2011 N Lance Hepler <[email protected]> 
+
+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 2 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, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

contrib/hmmer-3.0/COPYRIGHT

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+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/
+
+
+
+

contrib/hmmer-3.0/INSTALL

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+Brief installation instructions 
+HMMER 3.0; March 2010
+SRE, Mon Mar 24 09:29:34 2008
+-------------------------------------------------------------
+
+These are quick installation instructions. For complete documentation,
+including customization and troubleshooting, see the Installation
+chapter in the HMMER User's Guide (Userguide.pdf).
+
+Starting from a source distribution, hmmer-3.0.tar.gz:
+ uncompress:                uncompress hmmer-3.0.tar.gz  
+ unpack:                    tar xf hmmer-3.0.tar
+ move into new directory:   cd hmmer-3.0
+ configure:                 ./configure
+ build:                     make
+ automated tests:           make check
+ automated install:         make install
+
+HMMER is developed primarily on Linux and Mac OS/X systems. It is
+tested on a variety of UNIX and UNIX-like operating systems. It is
+written in ANSI C99 conforming to POSIX standards. It is meant to be
+portable to any POSIX-compliant system with an ANSI C99 compiler,
+including all UNIX and Macintosh systems. It should also build on
+Windows systems with optional POSIX compatibility software installed,
+such as Cygwin.
+
+-------------------------------------------------------------
+Starting from a Subversion (SVN) working copy:
+
+If you have checked HMMER out from its Subversion repository, there's
+some additional stuff you need to do one-time-only in your new working
+directory:
+
+   ln -s easel/aclocal.m4 aclocal.m4
+   autoconf
+   (cd easel; autoconf)
+
+-------------------------------------------------------------
+Brief notes on different ways we configure HMMER during development:
+
+for production:      ./configure CC=icc LDFLAGS="-static"
+   icc (Intel C compiler) is best, for optimal performance
+
+for debugging:       ./configure --enable-debugging
+
+for profiling:       ./configure CFLAGS="-g -pg -O"
+                     make
+                     (run benchmark program; then gprof the program)
+
+-------------------------------------------------------------
+The HMMER development team
+HHMI Janelia Farm Research Campus
+http://hmmer.org/
+
+