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barriers - Compute local minima and energy barriers of a landscape ## INSTALLATION Typically, barriers in installed like this: ./configure ./make ./make install 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 'scripts/get_hashbits.pl' to optimize the hashsize given your RAM size and sequence length. ## PUBLICATIONS 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) Ligand support has been added with version 1.7.0, see M.T. Wolfinger, Ch. Flamm, I.L. Hofacker Efficient computation of cotranscriptional RNA-ligand interaction dynamics Methods, 2018 (doi: 10.1016/j.ymeth.2018.04.036) ## COPYRIGHT AND LICENCE Copyright (C) 2001 Ivo Hofacker, Christoph Flamm, Peter Stadler, Michael T. Wolfinger 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 <email@example.com>