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Table 2 The effects of codon usage bias on LRTs (n = 29)

From: Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family

   Model
   F equal F3×4 F codon
Estimates under model A   p0 = 0.427, p1 = 0.241
(p2 + p3) = 0.330
ω2 = 11.182
p0 = 0.452, p1 = 0.170
(p2 + p3) = 0.376
ω2 = 999
p0 = 0.469, p1 = 0.157
(p2 + p3) = 0.372
ω2 = 999
Estimates under M1a   p0 = 0.627, p1 = 0.372
ω0 = 0.193
p0 = 0.711, p1 = 0.288
ω0 = 0.126
p0 = 0.730, p1 = 0.269
ω0 = 0.113
Estimates under model A (ω2 = 1)   p0 = 0.437, p1 = 0.259 (p2 + p3) = 0.302
ω0 = 0.187
p0 = 0.480, p1 = 0.189 (p2 + p3) = 0.329
ω0 = 0.121
p0 = 0.505, p1 = 0.178 (p2 + p3) = 0.316
ω0 = 0.107
l Test 1: 35.44 53.78 54.38
  Test 2: 19.98 28.22 27.89
  1. 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.