Summary of the measures used to evaluate alignment quality that are discussed in this paper. "Independent Measures" are those that do not compare an alignment to a reference alignment, but compare the superimposed structures implied by an alignment. "Dependent Measures" compare an alignment to a reference alignment. The Graphical Display Tools highlight differences in alignment between the reference alignment and a test alignment. An example output is shown in Figure: 8. For definitions of terms used in this Figure, see Results.