Permutation Software
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GRAILPermGeno.py   Generates permuted genotypes using GRAILPerm data files
GRAILperm.R        R Script automates permutations from GRAILPermGeno.py.  Requires R/qtl

Analysis Software
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OutParser.py       Generates locus-specific P-values
CombineMaps.py     For one data set, samples output QTL maps for best P-values




GRAILPerm Data Files
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ailfam.txt         Parent IDs and offspring number, sex making up the simulated population
  Format:  each row gives parameters to create a type of offspring.  First two columns
           are parent IDs.  Third column is number of offspring to make for those parents
           of the sex in column four.  An easy way to use this is to always allow column
           three to equal one and list each offspring on a line.
ailmap.txt         marker positions for AIL markers in cM
  Format: each row is a chromosome.  Positions are in marker order
ailhaplo.txt       haplotype structure of final generation parents
  Format: each column is a parent.  First half column is one strand, second half another
markerphyspos.txt  physical positions of markers.  
  Format: Same as markerpos.txt, but with added column of physical positions


Mapping files are included for AIL hippocampus weight, coat color, and body weight.  Hippocampus also
includes a shortened version of the GRAILPerm data files to generate populations permuting only the
animals for which there are hippocampus weight observations in the original data (679 animals) and
for regenerating the subsampling by family and random data removal.

Mapping Data Files for R/qtl, "karl" format
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pheno.dat          original phenotypes for AIL data
geno.txt           original AIL genotypes
chr.dat            chromosome for each marker
markerpos.txt      position for each marker in cM
mnames.txt         name for each marker
pnames.txt         name for each phenotype