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 |