Analysis of the trees with the peeling algorithm

After the set of trees is generated, the next step in the analysis is to analyze the set of trees. The tool that is provided in this version of TreeLD is called treepeeling, a fast and efficient algorithm that is described in detail in Zöllner and Pritchard (2005). This algorithm is deterministic: i. e. multiple runs of the algorithm on the same set of trees will result in the same output.

When a tree set has been generated, the tree peeling options will be made available to the user in the Analysis Window. After clicking on the Tree peeling button, a dialog box will appear. The program will then require the input of parameters for the rate of mutation at the disease locus and the range of penetrance parameters that should be explored by the peeling algorithm. The disease mutation rate $\beta$ reflects the expected number of non-ancestral disease mutations in the ancestry of a randomly ascertained individual in a population of constant size and should range from 0.1 to 1. See Pritchard (2001) for a discussion about the implications for the choice of $\beta$. The choice of penetrance parameters depends on the analyzed phenotypes.