The program finds the order with the highest log10 likelihood L and prints out, in decreasing order of log10 likelihood, those orders whose associated log10 likelihoods are greater than or equal to (L - PUK_LIKE_TOL).
In particular, when the number of ordered loci is two, all possible orders of the specified loci are analyzed. When using this option, keep in mind that the number of orders analyzed is n!/f!, where n is the total number of loci and f is the number of ordered loci (and ! denotes factorial), and that analysis of all 360 orders of a typical set of 6 loci on chromosome 7 takes about 30 mins on a MICROVAX II; thus it is probably impractical to use this option with more than 6 inserted loci, except on a much faster computer.
When use_ord_file is set to 1 in the .par file, any orders incompatible with the orders database are eliminated prior to calculating likelihoods, which may make it feasible to use all with larger sets of loci.
One convenient use of this option is to position a new locus (which would be specified as the single inserted locus) with respect to a set of loci of known order.
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