================================= RIsearch2 ==================================

RIsearch2 is a program for fast RNA-RNA interaction prediction.
It uses a seed-and-extend approach, applying suffix arrays in the first stage to
locate initial seed matches (allowing for G-U wobble matches) and using dynamic
programming to extend those matches with a simplified energy model.


For installation instructions see file INSTALL


For instructions on how to run RIsearch2 see file Manual.pdf 


For testing the RIsearch2 with example data see test_suite/README


All correspondence should be addressed to: gorodkin@rth.dk


=============================== License ======================================

Copyright (c) 2016 by the contributors (see AUTHORS file)

  RIsearch2 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.

  RIsearch2 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 RIsearch2, see file COPYING.
  If not, see <http://www.gnu.org/licenses/>.



Note that libdivsufsort-2.0.1 which is included with the source comes with its
own separate license, included in COPYING.libdivsufsort-2.0.1

==============================================================================
