X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Flicense.extensions;fp=binaries%2Fsrc%2Fmafft%2Flicense.extensions;h=0000000000000000000000000000000000000000;hb=6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce;hp=9e14bea5e445a4e3cbc753d8867ef36fe2021978;hpb=48f0451143441afce738d887b0cde1fb5cdbc02e;p=jabaws.git diff --git a/binaries/src/mafft/license.extensions b/binaries/src/mafft/license.extensions deleted file mode 100644 index 9e14bea..0000000 --- a/binaries/src/mafft/license.extensions +++ /dev/null @@ -1,120 +0,0 @@ -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. - --------------------------------------------------------------------------------