|
Parameter estimates for branch-site model A from maximum likelihood analyses. |
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| Data Set |
Foreground branch |
f |
l |
Estimated parameters |
κ |
Positive selection (BEB) |
|
|
||||||
| RPS4Y1 |
Hsa Y1 |
14 |
-1275.00 |
p0 = 1 p1 = 0 (p2+p3 = 0), ω2 = 1 |
3.40 |
|
| RPS4Y2 |
Hsa Y2 |
8 |
-1233.73 |
p0 = 0 p1 = 0 (p2+p3 = 1), ω2 = 139.62 |
3.78 |
68H*, 70L*, 87I*, 108C*, 185A* |
| RPS4X |
Hsa X |
10 |
-1100.83 |
p0 = 1 p1 = 0 (p2+p3 = 0), ω2 = 1 |
--- b |
|
| RPS4 Y1/Y2 |
Hsa Y2 |
20 |
-1562.15 |
p0 = 0 p1 = 0 (p2+p3 = 1), ω2 a |
4.61 |
70I*, 185G* |
| Y2cluster |
20 |
-1570.33 |
p0 = 0 p1 = 1 (p2+p3 = 1), ω2 = 139.62 |
4.59 |
||
| RPS4 Y1/Y2/X |
Hsa Y2 |
28 |
-1971.13 |
p0 = 0 p1 = 0 (p2+p3 = 1), ω2 a |
3.21 |
68R*, 70I*, 87M*, 104D*, 108R*, 185G* |
| Y2cluster |
28 |
-1986.19 |
p0 = 0.942 p1 = 0.058 (p2+p3 = 0), ω2 = 1 |
3.12 |
||
| Y1Y2X No Hsa Y2 |
Y2cluster |
26 |
-1925.91 |
p0 = 0.939 p1 = 0.061 (p2+p3 = 0), ω2 = 1 |
3.16 |
|
| Y1Y2 No Hsa Y2 |
Y2cluster |
18 |
-1516.95 |
p0 = 0.901 p1 = 0.099 (p2+p3 = 0), ω2 = 1 |
4.62 |
|
| Y1Y2X Hsa |
Hsa Y2 |
8 |
-1619.84 |
p0 = 0.647 p1 = 0.021 (p2+p3 = 0.332), ω2 = 1 |
3.03 |
68R, 70I, 87M, 104D, 108R, 180L, 185G, 205F, 222L (P > 0.71) |
|
f for the number of free parameters; l for likelihood values; and κ for transitions/transversions. * Posterior probability >0.95. a ω cannot be estimated since there are no synonymous substitutions. b κ cannot be estimated since there are no transversions. | ||||||
Andrés et al. BMC Evolutionary Biology 2008 8:142 doi:10.1186/1471-2148-8-142 |
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