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Table 1 Evolutionary models for the different data sets

From: Evidence of recombination within human alpha-papillomavirus

Sequences Nucleotide Model Base Freqs Rates Invariable Sites Rate Variation
HPV16_L1 HKY+I A = 0.32 Ti/tv = 3.4 0.93 No
   C = 0.19    
   G = 0.19    
   T = 0.30    
HPV16_L2 TrN+I A = 0.31 R(a) = 1.0 0.89 No
   C = 0.22 R(b) = 6.5   
   G = 0.16 R(c) = 1.0   
   T = 0.31 R(d) = 1.0   
    R(e) = 3.9   
    R(f) = 1.0   
HPV16_E6 HKY+I A = 0.34 Ti/tv = 1.2 0.90 No
   C = 0.16    
   G = 0.22    
   T = 0.28    
HPV16_E7 HKY+I A = 0.31 Ti/tv= 7.0 0.95 No
   C = 0.21    
   G = 0.23    
   T = 0.25    
GI_L1 TVM+I+G A = 0.31 R(a) = 4.5 0.29 1.47
   C = 0.18 R(b) = 7.9   
   G = 0.19 R(c) = 3.4   
   T = 0.32 R(d) = 3.1   
    R(e) = 7.9   
    R(f) = 1.0   
GI_L2 GTR+I+G A = 0.29 R(a) = 2.4 0.17 1.67
   C = 0.21 R(b) = 4.6   
   G = 0.18 R(c) = 2.8   
   T = 0.32 R(d) = 1.7   
    R(e) = 3.3   
    R(f) = 1.0   
GI_E6 TVM+I+G A = 0.37 R(a) = 4.0 0.17 2.41
   C = 0.17 R(b) = 7.1   
   G = 0.21 R(c) = 2.8   
   T = 0.25 R(d) = 5.4   
    R(e) = 7.1   
    R(f) = 1.0   
GI_E7 HKY+G A = 0.33 Ti/tv = 1.2 0.00 0.85
   C = 0.23    
   G = 0.22    
   T = 0.22    
GII_L1 TVM+G A = 0.29 R(a) = 3.6 0.00 0.56
   C = 0.18 R(b) = 5.4   
   G = 0.22 R(c) = 2.3   
   T = 0.30 R(d) = 1.8   
    R(e) = 5.4   
    R(f) = 1.0   
GII_L2 GTR+G A = 0.25 R(a) = 2.3 0.00 0.84
   C = 0.24 R(b) = 4.8   
   G = 0.20 R(c) = 2.6   
   T = 0.30 R(d) = 1.4   
    R(e) = 3.2   
    R(f) = 1.0   
GII_E6 TVM+G A = 0.31 R(a) = 3.1 0.00 0.69
   C = 0.20 R(b) = 6.1   
   G = 0.23 R(c) = 2.2   
   T = 0.26 R(d) = 2.8   
    R(e) = 6.1   
    R(f) = 1.0   
GII_E7 TVM+G A = 0.31 R(a) = 3.7 0.00 1.25
   C = 0.22 R(b) = 7.5   
   G = 0.24 R(c) = 3.9   
   T = 0.23 R(d) = 5.0   
    R(e) = 7.5   
    R(f) = 1.0   
GIII_L1 TVM+I+G A = 0.24 R(a) = 2.7 0.29 0.83
   C = 0.23 R(b) = 4.8   
   G = 0.22 R(c) = 1.1   
   T = 0.30 R(d) = 0.9   
    R(e) = 4.8   
    R(f) = 1.0   
GIII_L2 TVM+I+G A = 0.22 R(a) = 1.5 0.33 1.85
   C = 0.26 R(b) = 3.1   
   G = 0.22 R(c) = 1.7   
   T = 0.30 R(d) = 0.7   
    R(e) = 3.1   
    R(f) = 1.0   
GIII_E6 TrN+G A = 0.32 R(a) = 1.0 0.00 0.68
   C = 0.22 R(b) = 2.2   
   G = 0.26 R(c) = 1.0   
   T = 0.20 R(d) = 1.0   
    R(e) = 4.0   
    R(f) = 1.0   
GIII_E7 HKY+I A = 0.27 Ti/tv = 1.1 0.32 Equal
   C = 0.20    
   G = 0.30    
   T = 0.23    
  1. I: Invariable sites. G: Rate variation. R(a):A-C. R(b): A-G. R(c): A-T. R(d): C-G. R(e): C-T. R(f): G-T. Ti/tv: Transition/transversion rate.