1 #program code; set to 1 when fine-mapping
          1 #data type for affecteds; 
	    #1, if haplotypes available 
	    #2, if only genotypes available

	   6 #number of loci listed in pedfile
	   2 #number of columns (i.e. fields) to skip in pedfile before 
             #marker genotypes begin

	  6 #number of markers from pedfile included in analysis
          2  1  3  4  5  6  #markers, IN MAP ORDER, where loci in
	                    #pedfile are assumed to be given in order
			    #1:n

	  1 #map type 
	    #1, if inter-locus distances in map order (1 fewer than incl. loci)
	    #2, if location on numberline, loci in map order
	    #3, if location on numberline, loci in pedfile order 
	    #(for types 2&3, locus farthest left should be assigned 
            #position 0.0)
	  0.2 0.2 0.2 0.2 0.2 #map, corresponding to map type 1 (all distances
                              #given in cM; see "Tips" for more info.)
	    #for map type=2, map is 0.0 0.2 0.4 0.6 0.8 1.0 
	    #for map type=3, map is 0.2 0.0 0.4 0.6 0.8 1.0 

	  20 #no. of affecteds given in pedfile
	  20 #no. affected individuals included in analysis
	   1  2  3  4  5  #Included affected individuals; subjects 
	   6  7  8  9 10  #are labeled in the order in which they are 
          11 12 13 14 15  #given in pedfile
	  16 17 18 19 20

	  1 #controls type
	    #1, if haplotypes available for controls
	    #2, if genotypes available for controls
            #3, if only allele freqs. avail. for controls, in pedfile order
	    #4, if only allele freqs. avail. for controls, in map order
	    #(see "Tips" for more info. on controls types 3/4)
          1 #order of Markov Chain modelling background LD (1 or 2)
          1 #Bayesian adjustment to estimated hap. freqs? (1=yes,0=no) 
	  15 #number of controls given in pedfile (only if cont. type is 1/2)
	  15 #number of controls used in analysis (only if cont. type is 1/2)
          21 22 23 24 25  #Included controls (only if cont. type is 1/2)
          26 27 28 29 30
          31 32 33 34 35
	  #if controls type is 3 or 4, i.e., only allele frequencies available,
	  #the following is the format for reading in the allele frequencies,
          #in place of the above (See "Tips" for more info. on this option):
	  #   #3 #controls type
	  #   #2   1 2 0.5 0.5
	  #   #2   1 2 0.5 0.5
	  #   #2   1 2 0.5 0.5
	  #   #2   1 2 0.5 0.5
	  #   #2   1 2 0.5 0.5
	  #   #2   1 2 0.5 0.5
	  #   #Each line corresponds to a marker. The first entry gives the
	  #   #number of alleles for that marker. This is followed by the list
	  #   #of alleles and a list of the corresponding frequencies (Note
	  #   #that the freqs. must sum to 1.0 for each marker)

	  1e-5 1e-5 1e-5 1e-5 1e-5  #per meiosis per locus mutation rates
          1e-5                      #(given in pedfile order)
	  1 #estimate heterogeneity parameter p? 
	    #1, to estimate p
	    #0, to fix p at initial value
	  0.25 #initial value for p (between 0.0 and 1.0) used for E-M alg.

	  #Names given to results files; each filename must be given on
	  #a new line (for descriptions, see "Output")
	  resout
	  ancout
	  maxout
	  oneout

	  0 #E_int; interval from the midpoint of which to grow
	    #ancestral hap; 0, if unknown (See "Search Procedures" 
            #for description and "Tips" for advice)

	  0.1 #max_res (See "Search Procedures" for description and 
              #"Tips" for advice)

	  20 #map_res (See "Search Procedures" for description and 
            #"Tips" for advice)

	  20 #max_cand (See "Search Procedures" for description and 
             #"Tips" for advice)

	  0 # anc_hap_known
	    #0, ancestral haplotypes will be estimated
	    #1, if set of ancestral haplotypes over which to search 
            #is specified
	    #if anc_hap_known=1, it is followed by the number of haplotypes
            #in the set and then the haplotypes themselves, e.g.,
            #    2 #number of candidate ancestral haplotypes to search over
	    #    1 2 1 1 2 1 
            #    1 2 2 2 2 2