data for locus pairs in case 0 block 554 the haplotype frequencies are condensed into counts of recombinant and non recombinant meioses in addition the system compiles indirect counting data for each locus pair in the family that are in cases 1 12 block 556 the list of genotype frequencies for the locus pair is sorted into proper order if the phase can be directly determined for the locus pair it is otherwise numerical methods are used to determine the phase of the locus pair the list of genotype frequencies is reordered to compensate for the phase the haplotype and genotype frequencies are then combined with data gathered from previous half sib families block 558 returning to fig5 b after the statistics have been gathered for each half sib family the system saves the family data block 522 the haplotype and genotype frequencies are combined with data gathered from previous families full sib returning to fig5 a after the statistics have been extracted for each family the system then proceeds to compute recombination frequencies and lod scores block 506 the compute functions compute recombination frequencies and lod scores for all locus pairs based on genotype frequencies and haplotype frequencies previously extracted from the raw data 0073 fig5 d is a flowchart providing further details of the compute recombination frequencies and lod scores processing of block 506 the system computes indirect counting data for locus pairs in cases 1 12 block 524 using genotype frequency data determined above recombination frequencies and lod scores are computed for each locus pair using iterative functions as noted above for each locus pair data has been gathered from several families the same locus pair may fall into different cases in different families for each case the recombination frequency and lod score is computed using.