Change into the **ci** subdirectory. Run the following set of commands:

% SRmapqtl -A -V -X mletest % Zmapqtl -A -V -M 6 % Eqtl -A -V -S 12.0 % cp mletest.eqt mletestPhase0.mqt % MImapqtl -A -V -I sMPrTseC -p 1 % MImapqtl -A -V -I sMPrtSeC

Compare the **mletestPhase*.mqt** files to the
true model in **mletest.qtl**. The first is the
model as estimated from composite interval mapping. The second is a reduced model in which **MImapqtl**
has deleted non-significant QTL. The third (*mletestPhase2.mqt*) contains a model after
**MImapqtl** has searched for more QTL. Is this final model closer to the true model than
the model obtained by the analysis in the previous section? How long did this whole process take?

Christopher Basten 2002-03-27