The 'extension' directory contains codes from (1) the Vienna RNA package (2) MXSCARNA (3) ProbConsRNA These packages are distributed under different licenses: ------------------------------------------------------------------------------- (1) The Vienna RNA package See ./extensions/mxscarna_src/vienna/COPYING and http://www.tbi.univie.ac.at/~ivo/RNA/ Disclaimer and Copyright The programs, library and source code of the Vienna RNA Package are free software. They are distributed in the hope that they will be useful but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Permission is granted for research, educational, and commercial use and modification so long as 1) the package and any derived works are not redistributed for any fee, other than media costs, 2) proper credit is given to the authors and the Institute for Theoretical Chemistry of the University of Vienna. If you want to include this software in a commercial product, please contact the authors. Reference: Ivo L Hofacker and Martin Fekete and Peter F Stadler Secondary structure prediction for aligned RNA sequences. J Mol Biol. 2002 vol. 319 (18) pp.3724-32 ------------------------------------------------------------------------------- (2) MXSCARNA See ./extensions/mxscarna_src/README and http://www.ncrna.org/software/mxscarna/ * Author Yasuo Tabei Department of Computational Biology, Graduate School of Frontier Science, The University of Tokyo and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) E-mail: scarna AT m.aist.go.jp * What is MXSCARNA MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a tool for fast structural multiple alignment of RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA. * License While its original source code is provided as free software, MXSCARNA contains the source codes of ProbCons and Rfold and the energy parameters of Vienna RNA package (version 1.5). The author thanks Dr. Chuong Do, Dr. Hisanori Kiryu and Dr. Ivo Hofacker, the authors of ProbCons, Rfold and Vienna RNA package respectively, and Institute for Theoretical Chemistry of the University of Vienna. The source code of Rfold is located in ./extensions/mxscarna_src/rfold-0.1, which includes energy parameters of Vienna RNA package in ./extensions/mxscarna_src/rfold-0.1/src/vienna. Energy parameters of Vienna RNA package are also included in the source code of MXSCARNA (./extensions/mxscarna_src/vienna). Please follow ./extensions/mxscarna_src/rfold-0.1/readme.txt file, which describes the license of Rfold, and ./extensions/mxscarna_src/rfold-0.1/src/vienna/COPYING file and ./extensions/mxscarna_src/vienna/COPYING file, which describe the copyright notice of the Vienna RNA package. The source code of ProbCons is located in ./extensions/mxscarna_src/probconsRNA. Please follow ./extensions/mxscarna_src/probcons/README. The original part of MXSCARNA is provided as free software. It 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. Permission is granted for research, educational, and commercial use and modification so long as 1) the package and any derived works are not redistributed for any fee, other than media costs, 2) proper credit is given to the authors of MXSCARNA, ProbCons, Rfold and Vienna RNA package, the Univeristy of Tokyo, Computational Biology Research Center (CBRC), AIST and Institute for Theoretical Chemistry of the University of Vienna. If you want to include this software in a commercial product, please contact the author. * Citation Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai A fast structural multiple alignment method for long RNA sequences. BMC bioinformatics 9:33 (2008) --------------------------------------------------------------------------------- (3) ProbCons See ./extensions/mxscarna_src/probconsRNA/README and http://probcons.stanford.edu/ * Author Chuong Do * License PROBCONS has been made freely available as PUBLIC DOMAIN software and hence is not subject to copyright in the United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions. PROBCONS is distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program. * Citation Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 2005 15:330-40. -------------------------------------------------------------------------------