Table 2

Summary statistics for detecting selection using branch-site models of PAML

Foreground branch

Null hypothesis

Alternative hypothesis



-ln L

Estimated parameters

-ln L

Estimated parameters


Branch A

46859.30

p0 = 0.66, p1 = 0.28 (p2+p3 = 0.06)

46851.6**

p0 = 0.69, p1 = 0.27 (p2+p3 = 0.04)

ω0 = 0.23, ω1 = ω2 = 1

ω0 = 0.23, ω1 = 1.00, ω2 = 999

Branch B

46854.00

p0 = 0.53, p1 = 0.22 (p2+p3 = 0.25)

46837.66**

p0 = 0.63, p1 = 0.26 (p2+p3 = 0.11)

ω0 = 0.23, ω1 = ω2 = 1

ω0 = 0.23, ω1 = 1.00, ω2 = 56.08

Branch C

46852.38

p0 = 0.53, p1 = 0.21 (p2+p3 = 0.36)

46831.76**

p0 = 0.64, p1 = 0.26 (p2+p3 = 0.10)

ω0 = 0.23, ω1 = ω2 = 1

ω0 = 0.23, ω1 = 1.00, ω2 = 526.55

Branch D

46859.11

p0 = 0.61, p1 = 0.26 (p2+p3 = 0.13)

46842.30**

p0 = 0.68, p1 = 0.27 (p2+p3 = 0.05)

ω0 = 0.23, ω1 = ω2 = 1

ω0 = 0.23, ω1 = 1.00, ω2 = 999

Branch E

46859.33

p0 = 0.70, p1 = 0.30 (p2+p3 < 0.01)

46859.33

p0 = 0.70, p1 = 0.30 (p2+p3 < 0.01)

ω0 = 0.23, ω1 = ω2 = 1

ω0 = 0.23, ω1 = ω2 = 1


Note: ** P <0.01, calculated from LRT.

Li et al. BMC Evolutionary Biology 2012 12:15   doi:10.1186/1471-2148-12-15

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