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Table 4 Log-likelihood values and parameter estimates under fixed-site models for flaA sequences

From: Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

Modela npa AIC rsb κb ωb
A (homogeneous model) 44 -6830.350 13748.700 1 2.093 0.062
B (different rs) 46 -6645.595 13383.190 rs2 = 4.473 rs3 = 1.614 2.286 0.049
C (different rs and πsc) 64 -6613.420 13354.840 rs2 = 5.595 rs3 = 1.608 2.262 0.046
D (different rs, κ, and ω) 50 -6613.537 13327.074 rs2 = 3.372 rs3 = 1.703 κ1 = 2.089 κ2 = 1.929 κ3 = 2.958 ω1 = 0.025 ω2 = 0.084 ω3 = 0.026
D2 (different rs and ω)d 47 -6617.228 13328.456 rs2 = 3.439 rs3 = 1.650 2.286 ω1 = 0.025 ω2 = 0.084 ω3 = 0.025
E (different rs, κ and ω, and different πs) 68 -6580.030 13296.060 rs2 = 3.944 rs3 = 1.688 κ1 = 1.929 κ2 = 1.929 κ3 = 3.005 ω1 = 0.023 ω2 = 0.083 ω3 = 0.025
  1. The three partitions correspond to the 1: N-terminal extreme (104 codons), 2: the central region (101 codons) and 3: the C-terminal extreme (80 codons).
  2. a np, number of parameters including 33 branch lengths.
  3. b rs, nucleotide substitution rate. The subscript corresponds to the three partitions of flaA sequences (rs1 is 1 in all models and it is not shown); κ: transition/transversion ratio; ω: dN/dS ratio.
  4. c πs, codon frequencies (data not shown).
  5. d Model D but with κ fixed to 2.286.