USING THE INDIVIDUAL PROGRAMS

For now it is best to use the individual programs rather than the front end. If you have no data, then you would use the programs in the following order:

1. Rmap, to create a random map of markers.

2. Rqtl, to generate a random genetic model for the map.

3. Rcross, to create a random cross.

4. LRmapqtl, to do a simple linear regression of the data on the markers.

5. SRmapqtl, to do a stepwise linear regression of the data on the markers to rank the markers.

6. Zmapqtl, to do interval or composite interval mapping.

7. Preplot, to reformat the output of the analysis for GNUPLOT.

8. GNUPLOT, to see the results graphically.

If you have data, then you might use the programs in the following order:

1. Rmap, to reformat the output of MAPMAKER or a standard input file.

2. Rcross, to reformat your data.

3. Qstats, to summarize missing data and calculate some basic statistics on your quantitative traits.

4. LRmapqtl, to do a simple linear regression of the data on the markers.

5. SRmapqtl, to do a stepwise linear regression of the data on the markers to rank the markers. This should be run with model 2.

6. Zmapqtl, to do interval or composite interval mapping. This should be run twice, once with model 3 and a second time with model 6.

7. Preplot, to reformat the output of the analysis for Gnuplot.

8. GNUPLOT, to see the results graphically.

We recommend that the new user tries a simulation to gain an understanding of the programs