File contents

Program name:
  murlet

Author:
  Hisanori Kiryu

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

Citation:
  Murlet: A practical multiple alignment tool for structural RNA sequences 
  Hisanori Kiryu; Yasuo Tabei; Taishin Kin; Kiyoshi Asai
  Bioinformatics 2007; doi: 10.1093/bioinformatics/btm146

Reference:
  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

  Match probability matrices are calculated 
  by using the code extracted from the ProbCons program (version 1.10)
  for ProbCons, see
    Chuong B Do, Mahathi S P Mahabhashyam, Michael Brudno, 
    and Serafim Batzoglou.
    ProbCons: Probabilistic consistency-based multiple sequence alignment.
    Genome Res, 15(2):33040, 2005.

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 source files in ./src/probcons/ directory
  contain the codes extracted from ProbCons (version 1.10)
  Please follow ./src/probcons/COPYING file,
  which describes the copyright notice of the ProbCons code

  The other part of the source codes is provided as Public Domain Software
  These source codes may be used, modified, or redistributed without
  restrictions.
 
  "murlet" 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 murlet_cygwin'
    cp murlet ../

  To determine the time_factor for a particular machine,
  run the shell script

    sh ./measure_time.sh

  then time_factor is obtained by taking the ratio
  time_factor = (elapsed_time)/(estimated_time)
  elapsed_time and estimated_time are displayed on console.
  Time estimate is reasonably correct for more than a few minutes.

  For example, time_factor ~ (567 sec / 71 sec) ~ 8 
  for cygwin on my machine.

Usage:
  murlet [options] <sequence file>

  <sequence file>:
    sequence file in multi fasta format
  
  options:
  -outfile=<outfile name>
    set output file name (default: murlet_out.txt)
    multiple alignment is printed in the Stockholm format.

  -logfile=<logfile name>
    set log file name (default: murlet_log.txt)

  -time_factor=<float>
     set scale factor <float> for internal time estimation (default: 1.0)

  -max_time=<float>
     set maximal time <float> in minutes for each pairwise alignment
     (default: 10.0)

  -max_memory=<float>
      set maximal memory <float> in mega bytes
      used for workspace of each DP computation (default 1500);

  These options can be set also using "./murlet_params.txt" file
  in the current directory. 
  Follow the format of this file in this directory.
  Token separation by spaces is important.
  Command line options have higher priorities than this file.

  Note that in the current implementation,
  the consensus structure is computed using the RNAalifold code
  from the multiple alignment.

Example: 
  ./murlet -outfile=out.txt -time_factor=20.0 -max_time=5.0 ./samples/tRNA.fa

Version History:
  0.1.1 03-Sep-2007 Fixed a bug in AlignProbData.cpp
                    that squares match probability
                    values during the probabilistic consistency
		    transformation of match probabilities.
  0.1   20-Nov-2006 Initial Release