Fig. 6

Trade-off curve and minimum coverage. Trade-off curves using the fasttree guide tree as in Fig. 5, plotted for different minimum coverage values required for sites to be included in the analysis. A minimum coverage of 1.0 implies that only complete columns with no gap and no unresolved characters are included. Bars on the right show the number of sites with the required minimum coverage for each family (Initial), as well as the maximum number of such sites reachable by optimization (Maximal). Bars show the median numbers over all families, intervals represent the first (25 %) and third (75 %) quartiles