Linkage group, Trait and number (#) of Extra QTLs can be selected for analysis however, the ENTER key must be pressed after typing a new value. The # Extra QTLs should be left at 0 until it is suspected that the data cannot be explained by a single QTL.

The (Means) button calculates and graphs the marker means, the (Regression) button performs and graphs marker regression analysis and attaches probabilities by running simulations(the more simulations the longer it takes), the (Interval) button performs and graphs interval mapping/flanking marker regression, and the (Expected) button overlays the actual marker means with the expected curve. It is possible to drag the expected curve around the graph (additive effect only), when the mouse button is released the residual sum of squares is displayed at the putative QTL position, if you don't like your result cancel the graph and re-select (Expected).

If #Extra QTLs is greater than 0 then that number of additional curves will be added to the (Expected) graph. All curves can then be dragged until the composite black line best fits the marker mean data as indicated by the residual sum of squares.

Analyses can also be invoked from the menu bar at the top of the Applet.