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 in multi fasta format options: -outfile= set output file name (default: murlet_out.txt) multiple alignment is printed in the Stockholm format. -logfile= set log file name (default: murlet_log.txt) -time_factor= set scale factor for internal time estimation (default: 1.0) -max_time= set maximal time in minutes for each pairwise alignment (default: 10.0) -max_memory= set maximal memory 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