Compute local minima and energy barriers of a landscape
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README

  barriers - Compute local minima and energy barriers of a landscape

  Copyright (C) 2001 Ivo Hofacker, Christoph Flamm, Peter Stadler

  barriers 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., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

Comments are welcome.

	- Ivo Hofacker, <ivo@tbi.univie.ac.at>


For an explanation of the algorithm, please see 

Ch. Flamm, I.L. Hofacker, P.F. Stadler, M.T. Wolfinger. Barrier trees of degenerate landscapes. 
Z. Phys. Chem., 216:155–173, 2002. (doi:10.1524/zpch.2002.216.2.155)

And now some useful information:

The barriers program uses a large static array for the hash table at the heart of the method.
The size of this hash and therefore the maximum size of the landscape you can analyse is set at 
compile time using the --with-hash-bits option of the configure script.
E.g.:
	./configure --with-hash-bits=27
will create a hash of 2^27 entries 

If you you need a hash size >2^27 you may have to set the --mcmodel=medium or -mcmodel=large option in gcc.
E.g.:
	./configure --with-hash-bits=29 CFLAGS='-mcmodel=medium'

You can use the script './get_hashbits.pl' to optimize the hashsize given your RAM size and sequence length