crimap documentation (version 2.4)

5.5 flipsn

For each locus order obtained by permuting an n-tuple (n >= 2) of adjacent loci within an initial (reference) locus order, displays the relative log10 likelihood (i.e. the log10 likelihood of the reference order, minus that of the permuted order).

For example, flips3 will find relative log10 likelihoods for all permutations involving triples of adjacent loci. (If n is omitted it is assumed to be 2). When n is 2, relative log10 likelihoods for all permutations are displayed; for higher values of n, only the permutations whose log10 likelihoods are at least that of the original order, less PUK_LIKE_TOL, are displayed. Note: the total # of orders which must be evaluated is 

                   (m - n + 1)(n! - (n-1)!) + (n - 1)!
where m is the total # of loci; thus it is impractical to use this option with large values of n. However, when use_ord_file is set to 1 in the .par file, permutations incompatible with the orders database are eliminated before calculating likelihoods, which will sometimes make it feasible to use larger n's.
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