NAME:     shrub (simulated history recombination upper bound)

SYNOPSIS: shrub [-d #] [-l #] [-a [#]] [-r #] [-g name] data-filename

OPTIONS: (See README-SHRUB for a more detailed description of the program.) 
  -d num    Display setting.
            0: Only display final results (default). 
            1: Display the original and the reduced data.
            2: Display as in 1 + display local bound matrices for global
               lower bounds.

  -l num    Fast lower bound method to be used in branch and bound.
            1: Hudson and Kaplan's bound (default).
            2: Approximate haplotype bound using distinct columns and rows.

  -a [num]  Obtain only a fast upper bound.
            num = the maximum number of row removals to be tried for every
            matrix in step 3' of the algorithm.  If a number is not specified,
            then all rows satisfying the condition in step 3' will be tried.

  -r num    Number of '-a 1' runs to be executed. (default is 1)

  -g name   Output an ARG with the computed number of recombination
            events into a file.  The output is in GML format.

EXAMPLES :  shrub datafile		   
            shrub -l 2 datafile		 
            shrub -a datafile		 
            shrub -a 2 datafile		 
            shrub -a 1 -r 5 datafile	 
            shrub -g graphics.gml datafile
            shrub -l 2 -a -g graphics.gml datafile            

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COMPILATION  :  A makefile is provided.  Simply typing "make" should 
                compile and link the program correctly on most platforms.
                The file macshrub is compiled for mac OSX and has been checked
                to run on snow-lepard.

DATA FILE    :  The first line of the data file is ignored.  If you like,
                you may put a description of the data there.
                The data should be in 0,1. (White space is allowed 
                between columns.)  Each sequence should be placed in a its
                own row.

EXAMPLE      :  An example data set (Kreitman.dat) is included.
                Try running "shrub -g Kreitman.gml Kreitman.dat" to 
                check that everything works correctly.

GRAPH VIEWING:  The GML file generated by the program can be viewed using
		a software of your choice.  We recommend VGJ (Visualizing
    		Graphs with Java), which can be downloaded free of charge 
		from the following webpage:

http://www.eng.auburn.edu/department/cse/research/graph_drawing/graph_drawing.html

	        NOTE:  You need to place the three GIF files ("*-ball.gif")
                       we provided, in the main VGJ directory.
                        
                1) Go to the main VGJ directory. (default: graph_drawing)
	        2) Start VGJ. (java EDU/auburn/VGJ/VGJ &)
            	3) Click on "Start a Graph Window" to bring up a
		   viewing window.
		4) On the menu bar, choose  "File" and then "Open (GML)."
                5) When you first open a GML file generated by
		   SHRUB, everything looks clustered at a point.
		   To expand the graph, choose
		   "Algorithms" --> "Tree" --> "Tree Down"
		6) Although step (4) makes the graph viewable, you
		   might still wish to rearrange certain things.  For
 		   example, some directed edges might point upward
		   instead of downward.  To rearrange the graph
	 	   manually, click on "Select Nodes" under "Mouse
		   Action," located to the left of the graph.  Using
	           the mouse, try rearranging the nodes to your liking. 
		   
BUG REPORT    :  Please report bugs to Yun S. Song <yssong@cs.ucdavis.edu>

AUTHOR        :  Yun S. Song
