---

5.10 twopoint

---

In the case of sex specific analyses, the output for each pair appears on three lines:

• the first has the locus names, followed by the maximum likelihood estimates, f and m, of the female and male recombination fractions, and the sex-specific LODS ( = log10 like(f,m) - log10 like(.5,.5)).

• The second line has the values of log10 like(r,m) - log10 like(.5,.5) for r = .001, .01, .05, and all multiples of .05 up through .5.

• The last line similarly has the values of log10 like(f,r) - log10 like(.5,.5).

Only pairs for which the LODS exceed PUK_LIKE_TOL are printed out. (You can get tables for all pairs by setting PUK_LIKE_TOL = 0.0). When SEX_EQ is 1, the sex-averaged recombination fractions, LODS, and log10 likelihoods are given instead. Haplotyped systems may be used for either locus in a pair.

If the loci within a system are not forced to have 0 distance, then maximum likelihood intralocus distances are found simultaneously with the maximum likelihood interlocus distances, and are subsequently held fixed at these values when likelihoods are calculated at the above specified interlocus distances.

If both ordered_loci and inserted_loci are specifed in the .par file, tables are only computed for pairs consisting of one locus from each list. This is convenient, for example, when one has just added data for a new set of loci to a file and wishes to look for linkages with the old loci. If only one list (either ordered_loci or inserted_loci) is non-empty, LOD tables are computed for all pairs of loci within that list.

previous section: 5.9 quick