Permutation Software
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SimplePerm.py      Shuffles the order of a set of phenotypes, with
                   the phenotypes of each animals on one line


Analysis Software
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OutParser.py       Generates locus-specific P-values
OutParserLI.py        Generates locus-specific P-values, interpolating 
                   LOD scores then calculating P.  Better for sparse genotypes.
CombineMaps.py     For permutations from multiple data sets, samples 1 output from each 
                      data set, calculates composite QTL maps for best P-values

Mapping files, in Karl format, are also included for TJL BXD strains for hippocampus weight
and for new BXD strains for body weight and coat color.