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Table 1 Parameter estimates and likelihood values under branch and branch-site models.

From: Molecular evolution of the cytochrome c oxidase subunit 5 A gene in primates

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

  1. 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.