1. A method for detecting polymorphism in a nucleic sequence comprising: receiving a first plurality of hybridization intensities for a first group of probes that are complementary to the nucleic acid sequence except that the first group of probes includes all possible monosubstitutions of positions in the sequence that are within n bases of a base in the nucleic sequence that is complementary to said polymorphism; receiving a second plurality of hybridization intensities for a second and third group of probes complementary to marker-specific regions upstream and downstream of the polymorphism in the nucleic acid sequence; and analyzing the first plurality of hybridization intensities and the second plurality of hybridization intensities.