Figure 1.

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