Visual analysis of trees

An advantage of the analysis performed by TreeLD is that the LD-signal is visualized in a unique way by the generated tree set. Clicking on a tree set will cause a pop-up window to appear, showing the tree at the location of interest. If the input is a case-control sample, the tips in this tree will be colored to indicate the case/control status of the tip. This allows the user to identify clades in the tree that have an overabundance of cases among their descendants.

It is specially informative to view the trees at the location with the highest posterior likelihood. For this purpose, you can click on the focal point with the highest likelihood in the displayed graph. This will cause a blue triangle to appear, as shown in figure 7. It will also highlight the tree set that has been generated at this spot for further inspection.

Analyzing the trees at this location provides an informal way to estimate the number of disease mutations, as every such cluster is the result of one disease mutation. Furthermore the user can assess which chromosomes carry which disease mutation by identifying the clade it belongs to. Clicking on any internal node in the tree will open a window, showing the length of sequence that is transmitted to all terminal decedents of that node. This visualizes the region that is most likely to carry a disease mutation.