Linked genes are sets of genes that are close to each other on chromosome maps, and are usually associated with each other. Some common examples are blonde hair and blue eyes, and red hair with freckles.
More complicated linked genes are mapped out with all combinations are listed before determining chance. This is because punnet squares and other dihybrid crosses do not take in account distance. To calculate the distance on a map, put one gene probability out of 100 and multiply it with the other gene probability. The resulting percentage is the map distance and the frequency those two genes will be together.