Table 1.

Simulation design.The table shows the treatments used in each of two simulation series, ASHIFT and RFREQ. Root frequencies indicates whether initial codon frequencies were drawn independently from the mutation-selection models applied to the tree. Balance indicates the simulated tree balace condition: BAL = balanced, BDP = birth-death balance, IMB = imbalanced

Series	Selective shifts	Root frequencies?	Taxa	Codons	Balance	Birth rate	Replicates per block
ASHIFT	1	No	10,20	300,600,900	BDP	0.5	20
	0	No	10,20	300,600,900	BDP	0.5	20
RFREQ	0	Yes	20	300	BAL, BDP, IMB	0.1, 0.5, 2.0, 5.0, 10.0	10