We will work with the files **mletest.map** and **mletest.cro** for this section.
We are going to analyze the data in three ways. The first will be to use
**MImapqtl** to find a model *de novo*. Then, we will use composite interval mapping
to find an initial model for multiple interval mapping. Finally, we will
use stepwise regression to determine an initial model and multiple interval mapping to complete the analysis.

Create a new subdirectory called **mletest2** in your **qwork** subdirectory. Within that
subdirectory, create three new subdirectories called **ci**, **mi** and **mr**. Place copies of
the data files
(**mletest.map** and **mletest.cro**) in each of these directories. In UNIX, you would do this:

% cd qwork % mkdir mletest2 % cd mletest2 % mkdir ci % mkdir mi % mkdir mr % cp ~/QTLCartUnix/example/mletest.* ci % cp ~/QTLCartUnix/example/mletest.* mi % cp ~/QTLCartUnix/example/mletest.* mr

- Multiple interval mapping from scratch
- Composite interval mapping preceeds multiple interval mapping
- Multiple regression preceeds multiple interval mapping
- Real Data