Program name:
  mccaskill_mea

Author:
  Hisanori Kiryu

  Computational Biology Research Center, 
  The National Institute of 
  Advanced Industrial Science and Technology (AIST), Japan.

Reference:
  Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai.
  Robust prediction of consensus secondary structures
  using averaged base pairing probability matrices.
  Bioinformatics. 2007 Feb 15;23(4):434-41.

  Base pair probability matrices are calculated 
  using the code extracted from the RNAalifold program of Vienna RNA
  package (version 1.5)
  for RNAalifold, see
    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

Lisense:
  The source files in ./src/alifold/ directory
  contain the codes extracted from the Viennea RNA package (version
  1.5).
 
  please follow ./src/alifold/COPYING file,
  which describes the copyright notice of the Vienna RNA package.

  The other part of the source codes is provided as Public Domain Software
  These source codes may be used, modified, or redistributed without
  restrictions.
 
  "mccaskill_mea" is distributed WITHOUT WARRANTY, expressed or implied.
  The author accepts NO LEGAL LIABILITY OR RESPONSIBILITY for
  loss due to reliance on the program.

Install:
  the program was tested using 
  gcc 4.0 on linux machines and gcc 3.4 on cygwin
  Some gcc specific features are currently used.
  
  cd ./src
  make  # For cygwin, please use 'make mccaskill_mea_cygwin' instead
  cp mccaskill_mea ../

Usage:
  mccaskill_mea [options] <sequence file>

  <sequence file>:
    sequence file in multi fasta format
  
  options:
  -outfile=<outfile name>
    set output file name (default: mccaskill_mea_out.txt)
  
  -alpha=<float number>
    set scale factor alpha of loop probability. (default: 0.91) 
    expected accuracy = alpha sum_i qi + 2 sum_i_j pij 
    set alpha to larger values for higher specificity, 
    smaller values for higher sensitivity 

Example: 
  ./mccaskill_mea -alpha=0.0 -outfile=out.txt ./samples/tRNA.fa

Version History:
  1.0 15-Nov-2006 Initial Release