To get started, select a set of traits from the top of the menu, then click 'Submit Cross' to change your starting options. At any time, you can change this set of available traits. Be warned that if you also have parents selected you will get error messages. Re-setting the parents will remove those messages.
Once you have selected a set of traits, read a general description of your system in the 'Overview' tab. That will explain what phenotypes you are working with. For each set of traits, you will be asked to identify the genetic structure of each population separately, then how the two interact.
To set up a cross, select a male and a female parent from the drop-down lists on the right. Initially, you will have just the Purebred colors, but after you run each cross, the offspring will be available for use in future crosses.
Next, click 'Submit' and the cross will be run. Move to the 'Current Cross' tab to see the results. There, you will see a table with the number of offspring with each phenotype and a graph showing the same information. Interpret these results as best you can before setting up another cross and going again.
In addition, the tab 'All Crosses' holds the data from every cross you've run (along with lines for the Purebred lines you started with). Use this tab to look back at past results and to select parents for your next breeding cross. When you are done, you can download the data from all of the crosses for your records.
As a final note: the results of these crosses are random (technically pseudo-random, but random enough for us). Thus, you should not expect the ratios to come out exactly like you would predict. Keep that in mind as you work through the results. No new mutations are introduced during the crosses.