Figure 1

Principles of MarkerSet and main parameters. a) MarkerSet selects markers in two windows separated by the Average Marker Interval (AMI), which is the whole genome size divided by the number of markers to select. The window size is a percentage of the AMI (20% by default). Shifting iteratively the windows by the AMI gives a full genome coverage. Different sets are created by using all the possible starting points (x and y). b) Several parameters and options are available in order to improve the sets quality. The space_plus and space_resampling parameters are used to enlarge the window size in case of low (or no) informativity: space_plus is set by default as 50% of the window size on each side. This is automatically performed if the informativity of markers available is lower than the defined informativity threshold. Space_resampling is used to iteratively enlarge window size (by default +1 cM on each side at each step) until markers with informativity higher than the defined resampling threshold are found (resampling option mode).