A new version to identify instances on both strands

• GALF-P Ver 1.1 is an extension for the original GALF-P. The new version identifies GALF (assuming one instance per sequence) and post-processing results with examination on forward strands or both strands including the reverse ones.
• Download: Win32 version

Usage

• In cmd: GALF_P_VER1.1.exe -w width -i input_file -o output_file [-l MAXLEN\-m MAXINS\-b BETA\- r MAXRUN] [-g Gen\-p Pop\-u Muta\-c Cross] [-f Flag\-A PGALF\-d DFLAG]
• All the arguments are the same as those in the original GALF-P except that -d is added to indicate whether the program reports only forward strand search results or includes forward strand results as well.
  
• Options:
  

  Compulsary arguments:
  	-w		width is the desired motif width (input by the user)
  	-i		input_file is the fasta input file to read in
  	-o		output_file is the output file to store the results in detail (refer to the examples for more details)
  Optional configuration arguments:
  	-l		MAXLEN--maximal sequence length (>=500(default: 1000))
  	-m		MAXINS--maximal number of possible instances in each sequence (default: 20; >=1)
  	-b		BETA--the fitness gain threshold in post processing(default: 0.001; >=0)
  	-r		MAXRUN--number of runs of GALF (default: 20; >=5) before post processing
  	-g		Gen--maximal generation (>=300(default))
  	-p		Pop--population size (>=500(default))
  	-u		Muta--mutation rate (>=0 and <= 1 (default: 0.9))
  	-c		Cross--crossover rate (>=0 and <= 1 (default: 0.3)
  Optional control arguments:
  	-f		Flag--to control whether post-processing (adding and/or removing) is performed: 0 (default): both adding and removing; 1: adding only; 2: none
  	-a		PGALF--whether to print the results of GALF to the output file: 0 (default): No; 1: Yes
  	-d		DFLAG--to report forward strand search results: 1 (default) or include reverse strand instances: 2
  Note: The convergence generation number is fixed at 50 in GALF. Both upper and lower cases for the arguments are acceptable. If the input parameters exceed the listed constraints, the corresponding parameters will be set automatically to be the maximal/minimal constrained values. The actual computation time will be recorded in the output file.