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Table 4 The effects of codon usage bias on LRT (n = 12)

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

   Model
   F equal F3x4 F codon
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
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
l Test 1: 22.85 33.78 35.27
  Test 2: 10.31 6.84 6.83
  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.