Figure 2

Overall alignment sensitivity. For each divergence distance and each tool, 1,000 replicates were used to calculate the mean and standard error of overall alignment sensitivity, which was defined as the fraction of ungapped, orthologous pairs of sites in the simulated alignment that were aligned correctly in an alignment produced by a tool (for details see Methods in [1]). A) overall sensitivity without constrained blocks and without insertion/deletion evolution; B) overall sensitivity without constrained blocks and with insertion/deletion evolution; C) overall sensitivity with constrained blocks and without insertion/deletion evolution; D) overall sensitivity with constrained blocks and with insertion/deletion evolution.