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Table 3 Log-likelihood values and parameter estimates for the codon-based models of nucleotide substitutions

From: Sca 1, a previously undescribed paralog from autotransporter protein-encoding genes in Rickettsia species

Model LnL Estimates of Parameters* Predicted positively selected sites¶
M0 (one-ratio) -7522 ω = 0.91 None
M1 (neutral) -7491 ω0 = 0 (p0 = 0.46)
ω1 = 1 (p1 = 0.54)
Not allowed
M2 (selection) -7461 ω0 = 0 (p0 = 0.42)
ω1 = 1 (p1 = 0.48)
ω2 = 5.96 (p2 = 0.01)
 
M3 (discrete) -7461 ω0 = 0.06 (p0 = 0.56)
ω1 = 1.59 (p1 = 0.38)
ω2 = 7.61 (p2 = 0.06)
 
M7 (beta) -7491 P = 0.024 q = 0.020 Not allowed
7M8 (beta + ω) -7461 p = 0.024 q = 0.021 (p0 = 0.90)
ω = 5.75 (p1 = 0.10)
 
  1. * Sites attributed to the highest ω category with posterior probability > 0.90.
  2. ¶pi is the proportion of sites included in the site category.