1 The 'extension' directory contains codes from
3 (1) the Vienna RNA package
7 These packages are distributed under different licenses:
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10 (1) The Vienna RNA package
12 See ./extensions/mxscarna_src/vienna/COPYING and http://www.tbi.univie.ac.at/~ivo/RNA/
14 Disclaimer and Copyright
16 The programs, library and source code of the Vienna RNA Package are free
17 software. They are distributed in the hope that they will be useful
18 but WITHOUT ANY WARRANTY; without even the implied warranty of
19 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
21 Permission is granted for research, educational, and commercial use
22 and modification so long as 1) the package and any derived works are not
23 redistributed for any fee, other than media costs, 2) proper credit is
24 given to the authors and the Institute for Theoretical Chemistry of the
27 If you want to include this software in a commercial product, please contact
31 Ivo L Hofacker and Martin Fekete and Peter F Stadler
32 Secondary structure prediction for aligned RNA sequences.
33 J Mol Biol. 2002 vol. 319 (18) pp.3724-32
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38 See ./extensions/mxscarna_src/README and http://www.ncrna.org/software/mxscarna/
43 Department of Computational Biology,
44 Graduate School of Frontier Science,
45 The University of Tokyo
47 Computational Biology Research Center (CBRC),
48 National Institute of Advanced Industrial Science and Technology (AIST)
50 E-mail: scarna AT m.aist.go.jp
53 MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a tool for
54 fast structural multiple alignment of RNA sequences using progressive
55 alignment based on pairwise structural alignment algorithm of SCARNA.
58 While its original source code is provided as free software, MXSCARNA
59 contains the source codes of ProbCons and Rfold and the energy parameters
60 of Vienna RNA package (version 1.5).
61 The author thanks Dr. Chuong Do, Dr. Hisanori Kiryu and Dr. Ivo Hofacker,
62 the authors of ProbCons, Rfold and Vienna RNA package respectively,
63 and Institute for Theoretical Chemistry of the University of Vienna.
65 The source code of Rfold is located in ./extensions/mxscarna_src/rfold-0.1, which includes
66 energy parameters of Vienna RNA package in ./extensions/mxscarna_src/rfold-0.1/src/vienna.
67 Energy parameters of Vienna RNA package are also included in the source
68 code of MXSCARNA (./extensions/mxscarna_src/vienna). Please follow ./extensions/mxscarna_src/rfold-0.1/readme.txt
69 file, which describes the license of Rfold, and
70 ./extensions/mxscarna_src/rfold-0.1/src/vienna/COPYING file and ./extensions/mxscarna_src/vienna/COPYING file,
71 which describe the copyright notice of the Vienna RNA package.
72 The source code of ProbCons is located in ./extensions/mxscarna_src/probconsRNA. Please follow
73 ./extensions/mxscarna_src/probcons/README.
75 The original part of MXSCARNA is provided as free software. It is
76 distributed in the hope that it will be useful but WITHOUT ANY WARRANTY;
77 without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
80 Permission is granted for research, educational, and commercial use
81 and modification so long as
82 1) the package and any derived works are not redistributed for any fee,
83 other than media costs,
84 2) proper credit is given to
85 the authors of MXSCARNA, ProbCons, Rfold and Vienna RNA package,
86 the Univeristy of Tokyo,
87 Computational Biology Research Center (CBRC), AIST
88 and Institute for Theoretical Chemistry of the University of Vienna.
90 If you want to include this software in a commercial product, please
94 Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
95 A fast structural multiple alignment method for long RNA sequences.
96 BMC bioinformatics 9:33 (2008)
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101 See ./extensions/mxscarna_src/probconsRNA/README and http://probcons.stanford.edu/
107 PROBCONS has been made freely available as PUBLIC DOMAIN
108 software and hence is not subject to copyright in the United
109 States. This system and/or any portion of the source code
110 may be used, modified, or redistributed without restrictions.
111 PROBCONS is distributed WITHOUT WARRANTY, express or implied.
112 The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
113 loss due to reliance on the program.
116 Do CB, Mahabhashyam MS, Brudno M, Batzoglou S.
117 ProbCons: Probabilistic consistency-based multiple sequence alignment.
118 Genome Res. 2005 15:330-40.
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