False-Positive Rates for the Branch-Site Test in Simulations under the Null Model.
| Sequence Length | Internal Branch α | External Branch β |
| Tree I | ||
| 20 | 0.051 (0.68) | 0.043 (0.67) |
| 50 | 0.049 (0.64) | 0.041 (0.68) |
| 100 | 0.051 (0.62) | 0.048 (0.67) |
| 200 | 0.049 (0.62) | 0.042 (0.65) |
| 500 | 0.063 (0.55) | 0.040 (0.60) |
| 1,000 | 0.064 (0.50) | 0.049 (0.53) |
| 10,000 | 0.057 (0.49) | 0.056 (0.50) |
| Tree II | ||
| 20 | 0.046 (0.68) | 0.041 (0.72) |
| 50 | 0.045 (0.65) | 0.039 (0.70) |
| 100 | 0.043 (0.63) | 0.044 (0.68) |
| 200 | 0.050 (0.55) | 0.051 (0.62) |
| 500 | 0.052 (0.48) | 0.049 (0.57) |
| 1,000 | 0.056 (0.50) | 0.046 (0.51) |
| 10,000 | 0.053 (0.51) | 0.056 (0.51) |
| Sequence Length | Internal Branch α | External Branch β |
| Tree I | ||
| 20 | 0.051 (0.68) | 0.043 (0.67) |
| 50 | 0.049 (0.64) | 0.041 (0.68) |
| 100 | 0.051 (0.62) | 0.048 (0.67) |
| 200 | 0.049 (0.62) | 0.042 (0.65) |
| 500 | 0.063 (0.55) | 0.040 (0.60) |
| 1,000 | 0.064 (0.50) | 0.049 (0.53) |
| 10,000 | 0.057 (0.49) | 0.056 (0.50) |
| Tree II | ||
| 20 | 0.046 (0.68) | 0.041 (0.72) |
| 50 | 0.045 (0.65) | 0.039 (0.70) |
| 100 | 0.043 (0.63) | 0.044 (0.68) |
| 200 | 0.050 (0.55) | 0.051 (0.62) |
| 500 | 0.052 (0.48) | 0.049 (0.57) |
| 1,000 | 0.056 (0.50) | 0.046 (0.51) |
| 10,000 | 0.053 (0.51) | 0.056 (0.51) |
NOTE.—The test is conducted using the mixture of 0 and with critical value 2.71 at the 5% significant level. The proportion of data sets in which 2Δℓ = 0 is shown in parentheses.
False-Positive Rates for the Branch-Site Test in Simulations under the Null Model.
| Sequence Length | Internal Branch α | External Branch β |
| Tree I | ||
| 20 | 0.051 (0.68) | 0.043 (0.67) |
| 50 | 0.049 (0.64) | 0.041 (0.68) |
| 100 | 0.051 (0.62) | 0.048 (0.67) |
| 200 | 0.049 (0.62) | 0.042 (0.65) |
| 500 | 0.063 (0.55) | 0.040 (0.60) |
| 1,000 | 0.064 (0.50) | 0.049 (0.53) |
| 10,000 | 0.057 (0.49) | 0.056 (0.50) |
| Tree II | ||
| 20 | 0.046 (0.68) | 0.041 (0.72) |
| 50 | 0.045 (0.65) | 0.039 (0.70) |
| 100 | 0.043 (0.63) | 0.044 (0.68) |
| 200 | 0.050 (0.55) | 0.051 (0.62) |
| 500 | 0.052 (0.48) | 0.049 (0.57) |
| 1,000 | 0.056 (0.50) | 0.046 (0.51) |
| 10,000 | 0.053 (0.51) | 0.056 (0.51) |
| Sequence Length | Internal Branch α | External Branch β |
| Tree I | ||
| 20 | 0.051 (0.68) | 0.043 (0.67) |
| 50 | 0.049 (0.64) | 0.041 (0.68) |
| 100 | 0.051 (0.62) | 0.048 (0.67) |
| 200 | 0.049 (0.62) | 0.042 (0.65) |
| 500 | 0.063 (0.55) | 0.040 (0.60) |
| 1,000 | 0.064 (0.50) | 0.049 (0.53) |
| 10,000 | 0.057 (0.49) | 0.056 (0.50) |
| Tree II | ||
| 20 | 0.046 (0.68) | 0.041 (0.72) |
| 50 | 0.045 (0.65) | 0.039 (0.70) |
| 100 | 0.043 (0.63) | 0.044 (0.68) |
| 200 | 0.050 (0.55) | 0.051 (0.62) |
| 500 | 0.052 (0.48) | 0.049 (0.57) |
| 1,000 | 0.056 (0.50) | 0.046 (0.51) |
| 10,000 | 0.053 (0.51) | 0.056 (0.51) |
NOTE.—The test is conducted using the mixture of 0 and with critical value 2.71 at the 5% significant level. The proportion of data sets in which 2Δℓ = 0 is shown in parentheses.
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