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The effects of codon usage bias on LRT (n = 12) |
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| Model |
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| F equal |
F3x4 |
F codon |
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| Estimates under model A |
p0 = 0.51693, p1 = 0.152 (p2 + p3) = 0.330 ω2 = 11.182 |
p0 = 0.503, p1 = 0.102 (p2 + p3) = 0.393 ω2 = 14.201 |
p0 = 0.477, p1 = 0.095 (p2 + p3) = 0.426 ω2 = 999 |
|
| Estimates under M1a |
p0 = 0.732, p1 = 0.267 ω0 = 0.187 |
p0 = 0.793, p1 = 0.206 ω0 = 0.073 |
p0 = 0.794, p1 = 0.205 ω0 = 0.062 |
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| Estimates under model A (ω2 = 1) |
p0 = 0.492, p1 = 0.159 (p2 + p3) = 0.348 ω0 = 0.165 |
p0 = 0.537, p1 = 0.112 (p2 + p3) = 0.350 ω0 = 0.073 |
p0 = 0.533, p1 = 0.112 (p2 + p3) = 0.354 ω0 = 0.039 |
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| 2Δl |
Test 1: |
22.85 |
33.78 |
35.27 |
| Test 2: |
10.31 |
6.84 |
6.83 |
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Note: Branch-site model A was compared to site model M1a and model A with ω2 fixed to 1 for test 1 and 2, respectively. All tests are significant at 1%; with df = 2 and df = 1 for tests 1 and 2, respectively. | ||||
Levasseur et al. BMC Evolutionary Biology 2006 6:92 doi:10.1186/1471-2148-6-92 |
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