Table 1

Parameter estimates and likelihood values under branch and branch-site models.

Model

P

likelihood

Parameters estimated

Positively selected sites


Branch Models

1

-1431.66

ω all branches = 0.048

N/A

2

-1431.41

ω placental mammals = 0.054; background = 0.04

N/A

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

Open Data