Average missing branch rates and running times for 1000-taxon model conditions. The average missing branch rates and running times (in minutes) for the supertree methods for the 1000-taxon model conditions as a function of scaffold density. The standard error is shown for the missing branch rates, and the standard deviation is shown for the running times. Averages are computed only on replicates where there is sufficient taxonomic overlap to perform an accurate supertree analysis. n = 10 for all scaffold densities except n = 7 for the 20% scaffold density, and n = 9 for 50% scaffold density.