You can now input multiple pairs of coordinated Locus and Pedigree files. This is useful, for example, if you have pedigrees from different ethnic groups, and thus with different allele frequencies. Another common occurrence is to have pedigrees that were genotyped in different laboratories, and thus have differing allele sets.

To use this feature, the number of loci, their names, and their map positions must be identical for all locus and pedigree files. Between any of the pairs of coordinated locus and pedigree files, at any marker locus, the number of alleles, their names, and their frequencies may differ. However, if there is a trait locus, its data
must be indentical in all the locus files. If you have, for example, three pairs of locus and pedigree files, then set the first value in batch items #10 and #11 to "**3" (without the quotes) and follow this with the file names in order. To be concrete, using the lines:



would cause SimWalk2 to analyze all pedigrees in the file using the data in the file, and would similarly coordinate between pedigree-2.dat and locus-2.dat, etc. Any overall analysis involving the pedigrees from all three files would be computed appropriately. (Note that strictly speaking, parametric LOD scores computed using different allele frequencies are not summable. However, as is common, we ignore this subtlety.)

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