
seed used = 140084185

K12                                  ATG GTT ACT TAT CCC TGT CTA ACC AGT CGC CGC TTT CAA TTA GCT TTA ATC CAT CGA CGG GTC GTT GAT AAA CGT ACA TCC ATG CAC TCC CGT ACG GCG TCT GAA TCA ACT GGC GCG CGT ATT CAC CGC CCC TGG TGC GCA AGG CAT CAA GTT CGG CCA GCG TGG CGT TGT CAA TAC GAT AAA CTT CAC CGT GTA CCG TTC CGT TCC CCG GAA CTG CGC CTG GAT AGT GGC CCA GGC TAT ACA ACT GGT AGT TAT CGA TAC 
S2457T                               ATT ATT ACT TAT CCC TGT CTA ACC AGT CGC CGC TTT CAA TTA GCT TTA ATC CAT CGA CGG GTC GTT GAT AAA CGT ACA TCC ATG CAC TCC CAT ACG GCG TCT GAA TCA ACT GGC GCG CGT ATT CAC CGC CCC TGG TGC GCA AGG CAT CAA GTT CGG CCA GCG TGG CGT TGT CAA TAC GAT AAA CTT CAC CGT GTA CCG TTC CGT TCC CCG GAA CTG CGC CTG GAT AGT GGC CCA GGC TAT ACA ACT GGT AGT TAT CGA TAC 
O157                                 AGG GTT ACT TAT CCC TGT CTA ACC AGT CGC CGC TTT CAA TTA GCT TTA ATC CAT CGA CGG GTC GTT GAT AAA CGT ACA TCC ATG CAC TCC CGT ACG GCG TCT GAA TCA ACT GGC GCG CGT ATT CAC CGC CCC TGG TGC GCA AGG CAT CAA GTT CGG CCA GCG TGG CGT TGT CAA TAC GAT AAA CTT CAC CGT GTA CCG TTC CGT TCC CCG GAA CTG CGC CTG GAT AGT GGC CCA GGC TAT ACA ACT GGT AGT TAT CGA TAC 
EDL933                               AGG GTT ACT TAT CCC TGT CTA ACC AGT CGC CGC TTT CAA TTA GCT TTA ATC CAT CGA CGG GTC GTT GAT AAA CGT ACA TCC ATG CAC TCC CGT ACG GCG TCT GAA TCA ACT GGC GCG CGT ATT CAC CGC CCC TGG TGC GCA AGG CAT CAA GTT CGG CCA GCG TGG CGT TGT CAA TAC GAT AAA CTT CAC CGT GTA CCG TTC CGT TCC CCG GAA CTG CGC CTG GAT AGT GGC CCA GGC TAT ACA ACT GGT AGT TAT CGA TAC 


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b4223.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 87
# site patterns = 47
    1    1    3    3    2    2    1    1    3    4    1    3    2    1    1
    2    2    2    1    2    3    2    5    2    3    1    3    1    1    3
    1    2    1    3    1    2    1    1    1    2    2    1    1    2    1
    2    1

1       
K12                   ATG GTT ACT TAT CCC TGT CTA ACC AGT CGC TTT CAA TTA GCT ATC CAT CGA CGG GTC GTT GAT AAA CGT ACA TCC ATG CAC CGT ACG GCG TCT GAA TCA GGC ATT TGG TGC GCA AGG CCA TAC CTT GTA CCG TTC CTG GGT 
S2457T                ..T A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
O157                  .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
EDL933                .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT  1  1  1  1 | Ser TCT  1  1  1  1 | Tyr TAT  3  3  3  3 | Cys TGT  2  2  2  2
    TTC  1  1  1  1 |     TCC  3  3  3  3 |     TAC  2  2  2  2 |     TGC  1  1  1  1
Leu TTA  2  2  2  2 |     TCA  1  1  1  1 | *** TAA  0  0  0  0 | *** TGA  0  0  0  0
    TTG  0  0  0  0 |     TCG  0  0  0  0 |     TAG  0  0  0  0 | Trp TGG  2  2  2  2
--------------------------------------------------------------------------------------
Leu CTT  1  1  1  1 | Pro CCT  0  0  0  0 | His CAT  2  3  2  2 | Arg CGT  6  5  6  6
    CTC  0  0  0  0 |     CCC  2  2  2  2 |     CAC  3  3  3  3 |     CGC  4  4  4  4
    CTA  1  1  1  1 |     CCA  2  2  2  2 | Gln CAA  3  3  3  3 |     CGA  2  2  2  2
    CTG  2  2  2  2 |     CCG  2  2  2  2 |     CAG  0  0  0  0 |     CGG  2  2  2  2
--------------------------------------------------------------------------------------
Ile ATT  1  3  1  1 | Thr ACT  3  3  3  3 | Asn AAT  0  0  0  0 | Ser AGT  3  3  3  3
    ATC  1  1  1  1 |     ACC  1  1  1  1 |     AAC  0  0  0  0 |     AGC  0  0  0  0
    ATA  0  0  0  0 |     ACA  2  2  2  2 | Lys AAA  2  2  2  2 | Arg AGA  0  0  0  0
Met ATG  2  1  1  1 |     ACG  1  1  1  1 |     AAG  0  0  0  0 |     AGG  1  1  2  2
--------------------------------------------------------------------------------------
Val GTT  3  2  3  3 | Ala GCT  1  1  1  1 | Asp GAT  3  3  3  3 | Gly GGT  1  1  1  1
    GTC  1  1  1  1 |     GCC  0  0  0  0 |     GAC  0  0  0  0 |     GGC  3  3  3  3
    GTA  1  1  1  1 |     GCA  1  1  1  1 | Glu GAA  2  2  2  2 |     GGA  0  0  0  0
    GTG  0  0  0  0 |     GCG  3  3  3  3 |     GAG  0  0  0  0 |     GGG  0  0  0  0
--------------------------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: K12            
position  1:    T:0.21839    C:0.36782    A:0.19540    G:0.21839
position  2:    T:0.19540    C:0.26437    A:0.22989    G:0.31034
position  3:    T:0.35632    C:0.25287    A:0.21839    G:0.17241

#2: S2457T         
position  1:    T:0.21839    C:0.36782    A:0.20690    G:0.20690
position  2:    T:0.19540    C:0.26437    A:0.24138    G:0.29885
position  3:    T:0.36782    C:0.25287    A:0.21839    G:0.16092

#3: O157           
position  1:    T:0.21839    C:0.36782    A:0.19540    G:0.21839
position  2:    T:0.18391    C:0.26437    A:0.22989    G:0.32184
position  3:    T:0.35632    C:0.25287    A:0.21839    G:0.17241

#4: EDL933         
position  1:    T:0.21839    C:0.36782    A:0.19540    G:0.21839
position  2:    T:0.18391    C:0.26437    A:0.22989    G:0.32184
position  3:    T:0.35632    C:0.25287    A:0.21839    G:0.17241

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       4 | Ser S TCT       4 | Tyr Y TAT      12 | Cys C TGT       8
      TTC       4 |       TCC      12 |       TAC       8 |       TGC       4
Leu L TTA       8 |       TCA       4 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       0 |       TAG       0 | Trp W TGG       8
------------------------------------------------------------------------------
Leu L CTT       4 | Pro P CCT       0 | His H CAT       9 | Arg R CGT      23
      CTC       0 |       CCC       8 |       CAC      12 |       CGC      16
      CTA       4 |       CCA       8 | Gln Q CAA      12 |       CGA       8
      CTG       8 |       CCG       8 |       CAG       0 |       CGG       8
------------------------------------------------------------------------------
Ile I ATT       6 | Thr T ACT      12 | Asn N AAT       0 | Ser S AGT      12
      ATC       4 |       ACC       4 |       AAC       0 |       AGC       0
      ATA       0 |       ACA       8 | Lys K AAA       8 | Arg R AGA       0
Met M ATG       5 |       ACG       4 |       AAG       0 |       AGG       6
------------------------------------------------------------------------------
Val V GTT      11 | Ala A GCT       4 | Asp D GAT      12 | Gly G GGT       4
      GTC       4 |       GCC       0 |       GAC       0 |       GGC      12
      GTA       4 |       GCA       4 | Glu E GAA       8 |       GGA       0
      GTG       0 |       GCG      12 |       GAG       0 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.21839    C:0.36782    A:0.19828    G:0.21552
position  2:    T:0.18966    C:0.26437    A:0.23276    G:0.31322
position  3:    T:0.35920    C:0.25287    A:0.21839    G:0.16954

Codon frequencies under model, for use in evolver:
  0.01541164  0.01084979  0.00937027  0.00727429
  0.02148289  0.01512395  0.01306159  0.01013992
  0.01891428  0.01331565  0.00000000  0.00000000
  0.02545255  0.01791859  0.00000000  0.01201360
  0.02595644  0.01827333  0.01578151  0.01225144
  0.03618170  0.02547192  0.02199847  0.01707776
  0.03185563  0.02242636  0.01936822  0.01503586
  0.04286745  0.03017869  0.02606341  0.02023344
  0.01399214  0.00985047  0.00850722  0.00660429
  0.01950420  0.01373096  0.01185855  0.00920598
  0.01717217  0.01208921  0.01044068  0.00810527
  0.02310824  0.01626820  0.01404981  0.01090709
  0.01520885  0.01070703  0.00924698  0.00717858
  0.02120022  0.01492495  0.01288973  0.01000650
  0.01866541  0.01314045  0.01134857  0.00881007
  0.02511765  0.01768282  0.01527153  0.01185553



Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
S2457T              -1.0000 (0.0157 0.0000)
O157                -1.0000 (0.0052 0.0000)-1.0000 (0.0210 0.0000)
EDL933              -1.0000 (0.0052 0.0000)-1.0000 (0.0210 0.0000)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, 4));   MP score: 4
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):   -375.638609     +0.000000
   5..6     6..1     6..2     5..7     7..3     7..4  
  0.00531  0.00000  0.03744  0.00687  0.00000  0.00000  2.19615  0.00000  0.92339  1.00000 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.04964

((1: 0.000004, 2: 0.037444): 0.005313, (3: 0.000004, 4: 0.000004): 0.006873);

((K12: 0.000004, S2457T: 0.037444): 0.005313, (O157: 0.000004, EDL933: 0.000004): 0.006873);

Detailed output identifying parameters

kappa (ts/tv) =  2.19615


dN/dS for site classes (K=3)

p:   0.00000  0.92339  0.07661
w:   1.00000  1.00000999.00000

dN & dS for each branch

 branch           t        S        N    dN/dS       dN       dS   S*dS   N*dN

   5..6       0.005     76.1    184.9  77.4543   0.0025   0.0000    0.0    0.5
   6..1       0.000     76.1    184.9  77.4543   0.0000   0.0000    0.0    0.0
   6..2       0.037     76.1    184.9  77.4543   0.0175   0.0002    0.0    3.2
   5..7       0.007     76.1    184.9  77.4543   0.0032   0.0000    0.0    0.6
   7..3       0.000     76.1    184.9  77.4543   0.0000   0.0000    0.0    0.0
   7..4       0.000     76.1    184.9  77.4543   0.0000   0.0000    0.0    0.0


Positively selected sites (*: P>95%; **: P>99%)

            Pr(w>1)     post mean +- SE for w

     1 M      1.000**       998.980
     2 V      0.978*        977.232
    31 R      0.971*        970.138


Bayes Empirical Bayes (BEB) analysis
Positively selected sites (*: P>95%; **: P>99%)

            Pr(w>1)     post mean +- SE for w

     1 M      0.991**       8.929 +- 1.780
     2 V      0.935         8.489 +- 2.536
     3 T      0.627         5.923 +- 4.190
     4 Y      0.626         5.922 +- 4.190
     5 P      0.627         5.924 +- 4.190
     6 C      0.626         5.920 +- 4.191
     7 L      0.627         5.927 +- 4.189
     8 T      0.627         5.926 +- 4.189
     9 S      0.626         5.920 +- 4.190
    10 R      0.627         5.923 +- 4.190
    11 R      0.627         5.923 +- 4.190
    12 F      0.627         5.922 +- 4.190
    13 Q      0.627         5.923 +- 4.190
    14 L      0.627         5.929 +- 4.189
    15 A      0.627         5.923 +- 4.190
    16 L      0.627         5.929 +- 4.189
    17 I      0.627         5.926 +- 4.189
    18 H      0.626         5.918 +- 4.191
    19 R      0.627         5.927 +- 4.189
    20 R      0.627         5.927 +- 4.189
    21 V      0.627         5.926 +- 4.189
    22 V      0.627         5.924 +- 4.190
    23 D      0.626         5.922 +- 4.190
    24 K      0.627         5.926 +- 4.189
    25 R      0.626         5.920 +- 4.191
    26 T      0.627         5.927 +- 4.189
    27 S      0.627         5.925 +- 4.190
    28 M      0.627         5.926 +- 4.189
    29 H      0.626         5.922 +- 4.190
    30 S      0.627         5.925 +- 4.190
    31 R      0.935         8.488 +- 2.538
    32 T      0.627         5.928 +- 4.189
    33 A      0.627         5.928 +- 4.189
    34 S      0.626         5.922 +- 4.190
    35 E      0.627         5.925 +- 4.189
    36 S      0.627         5.928 +- 4.189
    37 T      0.627         5.923 +- 4.190
    38 G      0.627         5.925 +- 4.190
    39 A      0.627         5.928 +- 4.189
    40 R      0.626         5.920 +- 4.191
    41 I      0.627         5.924 +- 4.190
    42 H      0.626         5.922 +- 4.190
    43 R      0.627         5.923 +- 4.190
    44 P      0.627         5.924 +- 4.190
    45 W      0.627         5.926 +- 4.189
    46 C      0.627         5.923 +- 4.190
    47 A      0.627         5.927 +- 4.189
    48 R      0.627         5.927 +- 4.189
    49 H      0.626         5.918 +- 4.191
    50 Q      0.627         5.923 +- 4.190
    51 V      0.627         5.924 +- 4.190
    52 R      0.627         5.927 +- 4.189
    53 P      0.627         5.925 +- 4.189
    54 A      0.627         5.928 +- 4.189
    55 W      0.627         5.926 +- 4.189
    56 R      0.626         5.920 +- 4.191
    57 C      0.626         5.920 +- 4.191
    58 Q      0.627         5.923 +- 4.190
    59 Y      0.627         5.925 +- 4.190
    60 D      0.626         5.922 +- 4.190
    61 K      0.627         5.926 +- 4.189
    62 L      0.626         5.921 +- 4.190
    63 H      0.626         5.922 +- 4.190
    64 R      0.626         5.920 +- 4.191
    65 V      0.627         5.927 +- 4.189
    66 P      0.627         5.927 +- 4.189
    67 F      0.627         5.925 +- 4.190
    68 R      0.626         5.920 +- 4.191
    69 S      0.627         5.925 +- 4.190
    70 P      0.627         5.927 +- 4.189
    71 E      0.627         5.925 +- 4.189
    72 L      0.627         5.928 +- 4.189
    73 R      0.627         5.923 +- 4.190
    74 L      0.627         5.928 +- 4.189
    75 D      0.626         5.922 +- 4.190
    76 S      0.626         5.920 +- 4.190
    77 G      0.627         5.925 +- 4.190
    78 P      0.627         5.925 +- 4.189
    79 G      0.627         5.925 +- 4.190
    80 Y      0.626         5.922 +- 4.190
    81 T      0.627         5.927 +- 4.189
    82 T      0.627         5.923 +- 4.190
    83 G      0.626         5.922 +- 4.190
    84 S      0.626         5.920 +- 4.190
    85 Y      0.626         5.922 +- 4.190
    86 R      0.627         5.927 +- 4.189
    87 Y      0.627         5.925 +- 4.190



The grid (see ternary graph for p0-p1)

w0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

w0:   0.096  0.097  0.098  0.099  0.100  0.100  0.101  0.102  0.103  0.104
w2:   0.001  0.002  0.007  0.017  0.035  0.064  0.107  0.167  0.248  0.352

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.001 0.000 0.000
 0.003 0.001 0.001 0.000 0.000
 0.006 0.003 0.003 0.001 0.001 0.000 0.000
 0.011 0.007 0.006 0.003 0.002 0.001 0.001 0.000 0.000
 0.017 0.012 0.010 0.007 0.005 0.003 0.002 0.001 0.001 0.000 0.000
 0.026 0.020 0.017 0.012 0.010 0.007 0.005 0.003 0.002 0.001 0.001 0.000 0.000
 0.036 0.029 0.025 0.019 0.016 0.012 0.010 0.007 0.005 0.003 0.002 0.001 0.001 0.000 0.000
 0.049 0.040 0.036 0.028 0.025 0.019 0.016 0.012 0.010 0.006 0.005 0.003 0.002 0.001 0.001 0.000 0.000
 0.064 0.054 0.049 0.040 0.035 0.028 0.024 0.019 0.016 0.011 0.009 0.006 0.005 0.003 0.002 0.001 0.001 0.000 0.000

sum of density on p0-p1 =   1.000000
