Figure 3

Constraint coverage and sensitivity. For each divergence distance and each tool, 1,000 replicates were used to calculate the mean and standard error of constraint coverage and constraint sensitivity, which were defined as the coverage and sensitivity within interspersed constrained blocks (for details see Methods in [1]). A) constraint coverage without insertion/deletion evolution; B) constraint coverage with insertion/deletion evolution; C) constraint sensitivity without insertion/deletion evolution; D) constraint sensitivity with insertion/deletion evolution.