Figure 6.

Constraint specificity and local constraint sensitivity For each divergence distance and each tool, 1,000 replicates were used to calculate a mean and standard error of constraint specificity and local constraint sensitivity. Constraint specificity was defined as the fraction of unconstrained sites in the simulated alignment that were unaligned or gapped in an alignment produced by a tool. Local constraint specificity was defined as the constraint sensitivity for just the sites contained in an alignment produced by a tool (see Methods for details). A) constraint specificity without insertion/deletion evolution; B) constraint specificity with insertion/deletion evolution; C) local constraint sensitivity without insertion/deletion evolution; D) local constraint sensitivity with insertion/deletion evolution.