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Table 3 Comparison of alternative branch-class models (1, 2 and 3, Yang 1998[45]) and the branch-site model (4, Yang et al. 2005[46])

From: Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers

Model LnL Akaike Information Criterion dN/dS ratios (± standard errors)
1) ω1 = average dN/dS ratio across tree −15025 30052 0.015±0.001
2) ω1 = dN/dS ratio within classes −15000 30004 0.013 ±0.001
0.078±0.011
ω2 = dN/dS ratio between classes
3) ω1 = dN/dS ratio within class 1 −14989 29984 0.008±0.001
0.016±0.001
0.074±0.010
ω2 = dN/dS ratio within classes 2,3,4,5
ω3 = dN/dS ratio between classes
4) site class 0, ω1 = dN/dS of codons under equivalent purifying selection on both between class and within class branches. p 1  = proportion of codons −14945 29897 ω1 = 0.013±0.001
p 1  = 0.76±0.053
ω2 = 1.00±0.011
site class 2a, ω2 = dN/dS of codons with higher dN/dS ratios on between class branches than on within class branches (with dN/dS ratio = ω1). p 2  = proportion of codons p 2  = 0.24±0.053
(No codons were reconstructed to occupy site class 1 and 2b of model)