If selected when loading the data, Haploview computes single locus and multi-marker haplotype association tests. For case/control data, the chi square and p-value for the allele frequencies in cases vs. control are shown. For family trios, all probands (affected individual with genotyped parents) are used to compute TDT values. If the parenTDT option is selected, additional information is gained from parental phenotypes. More information about this method can be found in the Citations list in the About Haploview section.
The haplotype association test is performed on the set of blocks selected on the LD and haplotype tabs. Results are shown only for those haplotypes above the display threshold on the haplotype tab. Counts for both TDT and case control association tests are obtained by summing the fractional likelihoods of each individual for each haplotype. In other words, if a particular individual has been determined by the EM to have a 40% likelihood of haplotype A and 60% likelihood of haplotype B, 0.4 and 0.6 would be added to the counts for A and B respectively.
Additional information about the way in which pedigrees are filtered for TDT purposes can be found in the FAQ.
Haploview is not intended to be the only way of testing association results, but to provide a straightforward way to do simple association tests. It's always a good idea to try out multiple approaches to analyzing your data.
You can load a set of custom association tests in the format exported by Haploview and Tagger.