The mafft-6.6xx-with-extensions-src.tgz package has
the 'extensions' directory, which consists of the 
codes from:

(1) the Vienna RNA package 
(2) MXSCARNA
(3) ProbConsRNA

These are distributed under different licenses:

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(1) The Vienna RNA package 

See 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

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(2) MXSCARNA

See ./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 ./mxscarna_src/rfold-0.1, which
includes
 energy parameters of Vienna RNA package in
./mxscarna_src/rfold-0.1/src/vienna.
 Energy parameters of Vienna RNA package are also included in the source
 code of MXSCARNA (./mxscarna_src/vienna). Please follow
./mxscarna_src/rfold-0.1/readme.txt
 file, which describes the license of Rfold, and
 ./mxscarna_src/rfold-0.1/src/vienna/COPYING file and
./mxscarna_src/vienna/COPYING file,
 which describe the copyright notice of the Vienna RNA package.
 The source code of ProbCons is located in ./mxscarna_src/probconsRNA. Please
follow
 ./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)

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(3) ProbCons

See http://probcons.stanford.edu/ and ./mxscarna_src/probconsRNA/README

* 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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