Table 2.

Power of Contrast-FEL for Detecting Differences in Selection.

Simulation	N	$p\le 0.05$	$q\le 0.2$	Permutation $p\le 0.05$
Overall	139,753	0.418	0.319	0.361
Large effect	30,923	0.727	0.603	0.665
Large effect/sample size	14,265	0.902	0.860	0.867
Perfectly balanced trees	39,671	0.411	0.316	0.354
Perfectly ladder-like trees	27,439	0.479	0.378	0.417
Random/biological trees	72,643	0.399	0.298	0.343
Four-class simulations
Overall (omnibus)	18,141	0.355	0.276	0.379
Overall (any test)	18,141	0.415	N/A	N/A
Large effect (omnibus)	8,684	0.516	0.411	0.542
Large effect (any test)	8,684	0.587	N/A	N/A

Note.—N, total number of differentially selected sites in the set. Large effect is defined as having the absolute difference in simulated β rates of at least 1. Large sample size is defined as having at least three substitutions occurring along both test and reference branch sets.