If no penalty function is to be used, then it is important to specify the proper threshold for adding and dropping parameters. If the threshold is too low, then no QTL will be found. If too high, then MImapqtl will continue to find QTL until it reaches its upper limit. One can specify a low threshold and limit the number of QTL to find. Alternatively, one can perform a permutation test to get an inital threshold. We do this using a shell script to cycle through the Prune and MImapqtl commands for a predetermined number of repetitions.
Suppose qtlcart is the filename stem, and use as the work code, for the type I error rate, for the output column to process, and for the number of repetitions, then this snippet of psuedo-code will do a permutation analysis for MImapqtl.
echo "n-start" qtlcart.mim.ewt
Prune -A -V -i qtlcart.cro -b 2
MImapqtl -A -V -I -S -i qtlcart.crb
GetMaxLR.pl -r -C qtlcart.mim qtlcart.mim.ewt
echo "n-end" qtlcart.mim.ewt
The programs GetMaxLR.pl and EWThreshold.pl are Perl scripts that come with the UNIX distribution of the programs. There is also a D shell script called PermuteMI that can be modified for your particular data set. Use the script on the original data to obtain an initial threshold. This threshold can be used with MImapqtl and the SmprtSeR work code to find a QTL and compute residuals. From there, a new permutation test can be run to get a new threshold to search for more QTL.