Density of focal points

The tree-reconstruction step of TreeLD estimates the ARG of a region of interest by sequentially estimating the marginal trees at a number of focal points. Based on this estimate, the posterior distribution for the locus of disease mutation is generated. The quality of this estimate depends on the number of focal points it is based on. As the computation time of TreeLD increases linearly with the number focal points, it is important to select a number that is sufficient to provide good results. While theoretical calculations suggest that increasing the grid-density to up to 1,000 focal points/cM may still yield an improved result, it is questionable that using more focal points than there are markers in the dataset will improve the results noticeably. For our analyses we use between 10 and 50 focal points per cM.