+++ /dev/null
-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.
-
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