The relative average bootstrap support of phylogenetic trees is computed as the ratio of the average bootstrap support for the modified alignments divided by the bootstrap support obtained from the original alignment. Values larger than 1 indicate an increase in tree robustness. The curves show a distinct maximum that depends on the number of taxa and the topology of the tree. The maximum improvement increases with the number of taxa (indicated on the right margin of both panels for the highlighted curves). For clarity, error bars obtained from 100 replicates are shown only for N = 10 and N = 25 taxa. The tree topologies, caterpillar trees on the left and balanced trees on the right, are depicted by the insets.