Table 5.
MC Analysis for Cases of Discrepancy Between the Relative Frequency of Indels in the Simulation Model and MC Analysis Model
| θ simulated | Actual t | Observed t (ermse) | Estimated t (ermse) |
|---|---|---|---|
| 0.112 | 0.1 | 0.107 (0.0263) | 0.105 (0.0262) |
| 0.450 | 0.103 (0.0254) | 0.107 (0.0318) | |
| 0.112 | 0.2 | 0.206 (0.0306) | 0.204 (0.0336) |
| 0.450 | 0.205 (0.0346) | 0.245 (0.0716) | |
| 0.112 | 0.3 | 0.298 (0.0489) | 0.288 (0.0462) |
| 0.450 | 0.295 (0.0490) | 0.379 (0.1080) |
Pairs of sequences were simulated with the value of θ shown (the rate of indels relative to nucleotide substitutions). The value of θ assumed in the MC alignment analysis was 0.225. There were 50 replicates per value simulated.