Table 1 |
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|
Parameter estimates and likelihood values under branch and branch-site models. |
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|
Model |
P |
likelihood |
Parameters estimated |
Positively selected sites |
|
|
||||
|
Branch Models |
||||
|
1ω |
1 |
-1431.66 |
ω all branches = 0.048 |
N/A |
|
2ω |
2 |
-1431.41 |
ω placental mammals = 0.054; background = 0.04 |
N/A |
|
3ω |
3 |
-1408.70 |
ω anthropoid = 0.431; ω other placentals = 0.008; ω background = 0.042 |
N/A |
|
Free Ratio |
55 |
-1388.00 |
ω estimated independently for each branch (see Fig. 1) |
N/A |
|
Branch-site models |
||||
|
Model A |
4 |
-1399.23 |
p0 = 0.90; p1 = 0.012; p(2a+2b) = 0.085; ω0 = 0.021; ω1 = 1; background ω2a = 0.021; ω2b = 1; foreground, ω2a = ω2b = 4.61 |
5 (1.00); 38 (0.99); 41 (0.53); 64 (1.00); 70 (0.97) |
|
Model A (omega fixed) |
3 |
-1403.73 |
p0 = 0.80; p1 = 0.011; p(2a+2b) = 0.192; ω0 = 0.02; ω1 = 1; background ω2a = 0.02; ω2b = 1; foreground, ω2a = ω2b = 1 |
Not allowed |
|
|
||||
|
|
||||
|
P, number of parameters. Numbers in parentheses represent the posterior probability of each amino acid listed to be in the class of sites under positive selection. |
||||
|
Uddin et al. BMC Evolutionary Biology 2008 8:8 doi:10.1186/1471-2148-8-8 |
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