Table 3 |
|||
| Comparison of alternative branch-class models (1, 2 and 3, Yang 199845) and the branch-site model (4, Yanget al.200546) | |||
| 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. p1 = proportion of codons | −14945 | 29897 | ω1 = 0.013±0.001 |
| p1 = 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). p2 = proportion of codons | p2 = 0.24±0.053 | ||
| (No codons were reconstructed to occupy site class 1 and 2b of model) | |||
Eyres et al. BMC Evolutionary Biology 2012 12:148 doi:10.1186/1471-2148-12-148
