Running the Programs
There are two programs available: 

span_haplotype which finds the optimal subsets of markers by exhaustive search. This is only suitable for datasets with < 30 markers if you want the program to run in a few minutes. 
span_haplotype2 which finds suboptimal subsets of markers by greedy search. This is suitable for all datasets. The two programs produce the same answers on our test data, but we have not been able to prove if they are equivalent (Can you ?). 
Both programs have the same command-line options: 
      usage: span_haplotype2
	      -max            integer            The maximum subset size to consider. Default is # of markers
	      -top            integer            Report the top N subsets for each subset size (not available for span_haplotype2)
	      -minfreq        float              Ignore haplotypes with less than this frequency
	      -haplotypes     Readable File      Input file name
	      -help           switch             This help