Table 1.

Characterization of Simulated Data Sets.

ID	No. Taxa	Seq. Length (Codons)	Kappa	Omega
				M0	M3
S1	5	500	2	1.5	{1.50, 0.01, 0.80}
					{0.1, 0.5, 0.4}
S2	{25,100}	{100,1,000,10,000}	2	1.5	{1.50, 0.01, 0.50}
					{0.3, 0.6, 0.1}
S3	{60,120,240, 480}	500	2	1.5	{1.50, 0.01, 0.50}
					{0.3, 0.6, 0.1}

Note.—Sequences were simulated using the program evolver from the PAML package, five replicates, once under M0 and once under M3, in both cases on trees obtained with birth rate 0.2, death rate 0.05, sampling fraction 0.5, mutation rate 0.5, and branch lengths drawn from an exponential distribution with a mean of 0.1 substitutions per branch.