Two perl scripts are useful for parsing through the results file and
produce much shorter files which can be examined manually. 
These are useful when doing multiple program runs with the -m option
in Co-Bind.

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1. parse_results.pl 
usage: perl parse_results.pl <results_file_name>
Example: perl parse_results.pl sample.run > parse_out

The perl script generates a summary for each run. An example 
summary format is given below: 

START OF RUN: 17
# CONSENSUS  ACGATACTGA # INFORMATION   5.357 (base e)
# CONSENSUS  GCATGTCCGG # INFORMATION   4.424 (base e)
# >> Best iter for two units combined:  287
# >> Maximum conbined energy for both units (MaxUU): 0.847768
# >> MaxU1: 6.49107     MaxU2: 6.26696

The summary shows: 
a) The number of the run, 
b) Consensus obtained from the perceptron weights for the two	
   perceptrons (CONSENSUS) 
c) The information content of aligned sites for the two
   perceptrons (INFORMATION) 
d) Iteration which gives the maximum value of the objective
   function ("Best iter for two units combined:")
e) Maximum value of the combined objective function 
   (MaxUU)
f) Maximum value of objective function for each unit (MaxU1 and
   Max U2).
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2. sort_results.pl
usage: perl sort_results.pl <output_file_from_parse_results.pl>
		<number_of_top_scoring_runs_needed>
Example: perl sort_results.pl parse_out 10 > sort_out

This perl script sorts the results according to the maximum
objective function value (MaxUU), and outputs the summary of a
certain number top scoing runs. For summary format, see above.