Many statistical geneticists use linkage disequilibrium (LD) analysis as a method of genetic mapping. HelixTree software includes an interactive LD plot that enables the user to quickly determine the extent of disequilibrium between genetic marker pairs.

In this screen shot, a value of LD = 0 (indicating low linkage disequilibrium correlation) is shown by a blue coordinate cell, and LD = 1 (indicating high linkage disequilibrium correlation) is indicated by red cells. Other colors signify values between zero and one. The color guides at the top and the right side of the screen can be adjusted to narrow the range of the analysis.

By right clicking and dragging one can zoom into an area of LD correlation. By left clicking and dragging, one can select a group of markers and pop-up the Haplotype Frequency Estimation window as seen below. From the LD plot one can also determine groupings of markers which are in tight correlation with an individual marker or markers (tagging markers) within the grouping using the Carlson method for SNP tagging.