
seed used = 139999437

K12                                  ATG AAA TTA AAA ATA GTT GCG GTG GTT GTA ACT GGT TTG TTA GCT GCG AAC GTA GCA CAC GCT GCC GAA GTC TAT AAC AAG GAT GGT AAT AAA CTC GAC CTT TAT GGC AAG GTT ACC GCT CTA CGT TAT TTT ACT GAT GAT AAG CGT GAC GAT GGT GAT AAA ACT TAT GCC CGT CTC GGC TTT AAA GGA GAA ACG CAA ATC AAT GAT CAA ATG ATT GGT TTT GGT CAC TGG GAA TAT GAT TTT AAA GGC TAT AAC GAT GAA GCC AAC GGC TCG CGC GGC AAG AAT CTC 
S2457T                               ATG AAA TTA AAA ATA GTT GCG GTG GTT GTA ACT GGT TTG TTA GCT GCG AAC GTA GCA CAC GCT GCC GAA GTC TAT AAC AAG GAT GGT AAT AAA CTC GAC CTT TAT GGC AAG GTT ACC GCT CTA CGT TAT TTT ACT GAT GAT AAG CGT GAC GAT GGT GAT AAA ACT TAT GCC CGT CTC GGC TTT AAA GGA GAA ACG CAA ATC AAT GAT CAA ATG ATT GGT TTT GGT CAC TGG GAA TAT GAT TTT AAA GGC TAT AAC GAT GAA GCC AAC GGC TCG CGC GGC AAC AAG ACC 
Shig4337                             ATG AAA TTA AAA ATA GTT GCG GTG GTT GTA ACT GGT TTG TTA GCT GCG AAC GTA GCA CAC GCT GCC GAA GTC TAT AAC AAG GAT GGT AAT AAA CTC GAC CTT TAT GGC AAG GTT ACC GCT CTA CGT TAT TTT ACT GAT GAT AAG CGT GAC GAT GGT GAT AAA ACT TAT GCC CGT CTC GGC TTT AAA GGA GAA ACG CAA ATC AAT GAT CAA ATG ATT GGT TTT GGT CAC TGG GAA TAT GAT TTT AAA GGC TAT AAC GAT GAA GCC AAC GGC TCG CGC GGC AAC AAG ACC 
O157                                 ATG AAA TTA AAA ATA GTT GCG GTG GTT GTA ACT GGT TTG TTA GCT GCG AAC GTA GCA CAC GCT GCC GAA GTC TAT AAC AAG GAT GGT AAT AAA CTC GAC CTT TAT GGC AAG GTT ACC GCT CTA CGT TAT TTT ACT GAT GAT AAG CGT GAC GAT GGT GAT AAA ACT TAT GCC CGT CTC GGC TTT AAA GGA GAA ACG CAA ATC AAT GAT CAA ATG ATT GGT TTT GGT CAC TGG GAA TAT GAT TTT AAA GGC TAT AAC GAT GAA GCC AAC GGC TCG CGC GAC AAC AAG ACC 
EDL933                               ATG AAA TTA AAA ATA GTT GCG GTG GTT GTA ACT GGT TTG TTA GCT GCG AAC GTA GCA CAC GCT GCC GAA GTC TAT AAC AAG GAT GGT AAT AAA CTC GAC CTT TAT GGC AAG GTT ACC GCT CTA CGT TAT TTT ACT GAT GAT AAG CGT GAC GAT GGT GAT AAA ACT TAT GCC CGT CTC GGC TTT AAA GGA GAA ACG CAA ATC AAT GAT CAA ATG ATT GGT TTT GGT CAC TGG GAA TAT GAT TTT AAA GGC TAT AAC GAT GAA GCC AAC GGC TCG CGC GAC AAC AAG ACC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1472.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 96
# site patterns = 42
    2    6    2    1    3    2    1    2    3    5    1    3    4    1    2
    3    4    1    6    3    8    2    2    2    1    4    1    1    3    4
    1    1    2    1    1    1    1    1    1    1    1    1

1       
K12                   ATG AAA TTA ATA GTT GCG GTG GTA ACT GGT TTG GCT AAC GCA CAC GCC GAA GTC TAT AAG GAT AAT CTC GAC CTT GGC ACC CTA CGT TTT GGA ACG CAA ATC ATT TGG TCG CGC GGC AAG AAT CTC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..G AC. 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..G AC. 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ..C ..G AC. 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ..C ..G AC. 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  4  4  4  4  4 | Ser TCT  0  0  0  0  0 | Tyr TAT  6  6  6  6  6 | Cys TGT  0  0  0  0  0
    TTC  0  0  0  0  0 |     TCC  0  0  0  0  0 |     TAC  0  0  0  0  0 |     TGC  0  0  0  0  0
Leu TTA  2  2  2  2  2 |     TCA  0  0  0  0  0 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  1  1  1  1  1 |     TCG  1  1  1  1  1 |     TAG  0  0  0  0  0 | Trp TGG  1  1  1  1  1
--------------------------------------------------------------------------------------------------
Leu CTT  1  1  1  1  1 | Pro CCT  0  0  0  0  0 | His CAT  0  0  0  0  0 | Arg CGT  3  3  3  3  3
    CTC  3  2  2  2  2 |     CCC  0  0  0  0  0 |     CAC  2  2  2  2  2 |     CGC  1  1  1  1  1
    CTA  1  1  1  1  1 |     CCA  0  0  0  0  0 | Gln CAA  2  2  2  2  2 |     CGA  0  0  0  0  0
    CTG  0  0  0  0  0 |     CCG  0  0  0  0  0 |     CAG  0  0  0  0  0 |     CGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Ile ATT  1  1  1  1  1 | Thr ACT  3  3  3  3  3 | Asn AAT  3  2  2  2  2 | Ser AGT  0  0  0  0  0
    ATC  1  1  1  1  1 |     ACC  1  2  2  2  2 |     AAC  4  5  5  5  5 |     AGC  0  0  0  0  0
    ATA  1  1  1  1  1 |     ACA  0  0  0  0  0 | Lys AAA  6  6  6  6  6 | Arg AGA  0  0  0  0  0
Met ATG  2  2  2  2  2 |     ACG  1  1  1  1  1 |     AAG  4  4  4  4  4 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT  3  3  3  3  3 | Ala GCT  3  3  3  3  3 | Asp GAT  8  8  8  8  8 | Gly GGT  5  5  5  5  5
    GTC  1  1  1  1  1 |     GCC  3  3  3  3  3 |     GAC  2  2  2  3  3 |     GGC  5  5  5  4  4
    GTA  2  2  2  2  2 |     GCA  1  1  1  1  1 | Glu GAA  4  4  4  4  4 |     GGA  1  1  1  1  1
    GTG  1  1  1  1  1 |     GCG  2  2  2  2  2 |     GAG  0  0  0  0  0 |     GGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.15625    C:0.13542    A:0.28125    G:0.42708
position  2:    T:0.25000    C:0.15625    A:0.42708    G:0.16667
position  3:    T:0.41667    C:0.23958    A:0.20833    G:0.13542

#2: S2457T         
position  1:    T:0.15625    C:0.12500    A:0.29167    G:0.42708
position  2:    T:0.23958    C:0.16667    A:0.42708    G:0.16667
position  3:    T:0.40625    C:0.25000    A:0.20833    G:0.13542

#3: Shig4337       
position  1:    T:0.15625    C:0.12500    A:0.29167    G:0.42708
position  2:    T:0.23958    C:0.16667    A:0.42708    G:0.16667
position  3:    T:0.40625    C:0.25000    A:0.20833    G:0.13542

#4: O157           
position  1:    T:0.15625    C:0.12500    A:0.29167    G:0.42708
position  2:    T:0.23958    C:0.16667    A:0.43750    G:0.15625
position  3:    T:0.40625    C:0.25000    A:0.20833    G:0.13542

#5: EDL933         
position  1:    T:0.15625    C:0.12500    A:0.29167    G:0.42708
position  2:    T:0.23958    C:0.16667    A:0.43750    G:0.15625
position  3:    T:0.40625    C:0.25000    A:0.20833    G:0.13542

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      20 | Ser S TCT       0 | Tyr Y TAT      30 | Cys C TGT       0
      TTC       0 |       TCC       0 |       TAC       0 |       TGC       0
Leu L TTA      10 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG       5 |       TAG       0 | Trp W TGG       5
------------------------------------------------------------------------------
Leu L CTT       5 | Pro P CCT       0 | His H CAT       0 | Arg R CGT      15
      CTC      11 |       CCC       0 |       CAC      10 |       CGC       5
      CTA       5 |       CCA       0 | Gln Q CAA      10 |       CGA       0
      CTG       0 |       CCG       0 |       CAG       0 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       5 | Thr T ACT      15 | Asn N AAT      11 | Ser S AGT       0
      ATC       5 |       ACC       9 |       AAC      24 |       AGC       0
      ATA       5 |       ACA       0 | Lys K AAA      30 | Arg R AGA       0
Met M ATG      10 |       ACG       5 |       AAG      20 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      15 | Ala A GCT      15 | Asp D GAT      40 | Gly G GGT      25
      GTC       5 |       GCC      15 |       GAC      12 |       GGC      23
      GTA      10 |       GCA       5 | Glu E GAA      20 |       GGA       5
      GTG       5 |       GCG      10 |       GAG       0 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15625    C:0.12708    A:0.28958    G:0.42708
position  2:    T:0.24167    C:0.16458    A:0.43125    G:0.16250
position  3:    T:0.40833    C:0.24792    A:0.20833    G:0.13542

Codon frequencies under model, for use in evolver:
  0.01587039  0.00963559  0.00809714  0.00526314
  0.01080828  0.00656217  0.00551443  0.00358438
  0.02832044  0.01719455  0.00000000  0.00000000
  0.01067147  0.00647911  0.00000000  0.00353901
  0.01290792  0.00783695  0.00658567  0.00428069
  0.00879074  0.00533723  0.00448507  0.00291530
  0.02303396  0.01398490  0.01175202  0.00763881
  0.00867946  0.00526967  0.00442830  0.00287839
  0.02941312  0.01785797  0.01500670  0.00975435
  0.02003135  0.01216189  0.01022008  0.00664305
  0.05248721  0.03186723  0.02677919  0.01740647
  0.01977779  0.01200794  0.01009071  0.00655896
  0.04337907  0.02633729  0.02213218  0.01438591
  0.02954264  0.01793660  0.01507278  0.00979730
  0.07740920  0.04699844  0.03949449  0.02567142
  0.02916868  0.01770956  0.01488198  0.00967329



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 (0.0181 0.0000)
Shig4337            -1.0000 (0.0181 0.0000)-1.0000 (0.0000 0.0000)
O157                -1.0000 (0.0226 0.0000)-1.0000 (0.0045 0.0000)-1.0000 (0.0045 0.0000)
EDL933              -1.0000 (0.0226 0.0000)-1.0000 (0.0045 0.0000)-1.0000 (0.0045 0.0000)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 4
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):   -400.317500     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.01209  0.05521  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  1.41327  0.92309  0.00000  1.00000 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.06731

((1: 0.055207, (2: 0.000004, 3: 0.000004): 0.000000): 0.012087, (4: 0.000004, 5: 0.000004): 0.000000);

((K12: 0.055207, (S2457T: 0.000004, Shig4337: 0.000004): 0.000000): 0.012087, (O157: 0.000004, EDL933: 0.000004): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  1.41327


dN/dS for site classes (K=3)

p:   0.92309  0.00000  0.07691
w:   1.00000  1.00000999.00000

dN & dS for each branch

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

   6..7       0.012     63.1    224.9  77.7599   0.0051   0.0001    0.0    1.2
   7..1       0.055     63.1    224.9  77.7599   0.0235   0.0003    0.0    5.3
   7..8       0.000     63.1    224.9  77.7599   0.0000   0.0000    0.0    0.0
   8..2       0.000     63.1    224.9  77.7599   0.0000   0.0000    0.0    0.0
   8..3       0.000     63.1    224.9  77.7599   0.0000   0.0000    0.0    0.0
   6..9       0.000     63.1    224.9  77.7599   0.0000   0.0000    0.0    0.0
   9..4       0.000     63.1    224.9  77.7599   0.0000   0.0000    0.0    0.0
   9..5       0.000     63.1    224.9  77.7599   0.0000   0.0000    0.0    0.0


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

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

    93 G      0.977*        975.744
    94 K      0.973*        972.244
    95 N      0.970*        968.934
    96 L      1.000**       998.983


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

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

     1 M      0.671         6.452 +- 4.158
     2 K      0.671         6.448 +- 4.159
     3 L      0.672         6.457 +- 4.157
     4 K      0.671         6.448 +- 4.159
     5 I      0.671         6.454 +- 4.158
     6 V      0.670         6.446 +- 4.160
     7 A      0.672         6.456 +- 4.157
     8 V      0.672         6.456 +- 4.157
     9 V      0.670         6.446 +- 4.160
    10 V      0.671         6.454 +- 4.158
    11 T      0.671         6.449 +- 4.159
    12 G      0.670         6.445 +- 4.160
    13 L      0.672         6.457 +- 4.156
    14 L      0.672         6.457 +- 4.157
    15 A      0.670         6.446 +- 4.160
    16 A      0.672         6.456 +- 4.157
    17 N      0.671         6.448 +- 4.159
    18 V      0.671         6.454 +- 4.158
    19 A      0.671         6.454 +- 4.158
    20 H      0.671         6.451 +- 4.158
    21 A      0.670         6.446 +- 4.160
    22 A      0.671         6.452 +- 4.158
    23 E      0.670         6.445 +- 4.160
    24 V      0.671         6.452 +- 4.158
    25 Y      0.671         6.447 +- 4.160
    26 N      0.671         6.448 +- 4.159
    27 K      0.671         6.451 +- 4.158
    28 D      0.670         6.440 +- 4.162
    29 G      0.670         6.445 +- 4.160
    30 N      0.670         6.442 +- 4.161
    31 K      0.671         6.448 +- 4.159
    32 L      0.672         6.456 +- 4.157
    33 D      0.670         6.447 +- 4.160
    34 L      0.671         6.452 +- 4.158
    35 Y      0.671         6.447 +- 4.160
    36 G      0.671         6.452 +- 4.158
    37 K      0.671         6.451 +- 4.158
    38 V      0.670         6.446 +- 4.160
    39 T      0.671         6.454 +- 4.157
    40 A      0.670         6.446 +- 4.160
    41 L      0.672         6.457 +- 4.156
    42 R      0.671         6.453 +- 4.158
    43 Y      0.671         6.447 +- 4.160
    44 F      0.671         6.450 +- 4.159
    45 T      0.671         6.449 +- 4.159
    46 D      0.670         6.440 +- 4.162
    47 D      0.670         6.440 +- 4.162
    48 K      0.671         6.451 +- 4.158
    49 R      0.671         6.453 +- 4.158
    50 D      0.670         6.447 +- 4.160
    51 D      0.670         6.440 +- 4.162
    52 G      0.670         6.445 +- 4.160
    53 D      0.670         6.440 +- 4.162
    54 K      0.671         6.448 +- 4.159
    55 T      0.671         6.449 +- 4.159
    56 Y      0.671         6.447 +- 4.160
    57 A      0.671         6.452 +- 4.158
    58 R      0.671         6.453 +- 4.158
    59 L      0.672         6.456 +- 4.157
    60 G      0.671         6.452 +- 4.158
    61 F      0.671         6.450 +- 4.159
    62 K      0.671         6.448 +- 4.159
    63 G      0.671         6.454 +- 4.158
    64 E      0.670         6.445 +- 4.160
    65 T      0.672         6.457 +- 4.156
    66 Q      0.671         6.453 +- 4.158
    67 I      0.671         6.453 +- 4.158
    68 N      0.670         6.442 +- 4.161
    69 D      0.670         6.440 +- 4.162
    70 Q      0.671         6.453 +- 4.158
    71 M      0.671         6.452 +- 4.158
    72 I      0.671         6.447 +- 4.159
    73 G      0.670         6.445 +- 4.160
    74 F      0.671         6.450 +- 4.159
    75 G      0.670         6.445 +- 4.160
    76 H      0.671         6.451 +- 4.158
    77 W      0.672         6.458 +- 4.156
    78 E      0.670         6.445 +- 4.160
    79 Y      0.671         6.447 +- 4.160
    80 D      0.670         6.440 +- 4.162
    81 F      0.671         6.450 +- 4.159
    82 K      0.671         6.448 +- 4.159
    83 G      0.671         6.452 +- 4.158
    84 Y      0.671         6.447 +- 4.160
    85 N      0.671         6.448 +- 4.159
    86 D      0.670         6.440 +- 4.162
    87 E      0.670         6.445 +- 4.160
    88 A      0.671         6.452 +- 4.158
    89 N      0.671         6.448 +- 4.159
    90 G      0.671         6.452 +- 4.158
    91 S      0.672         6.459 +- 4.156
    92 R      0.672         6.456 +- 4.157
    93 G      0.950*        8.836 +- 2.293
    94 K      0.950*        8.835 +- 2.294
    95 N      0.950*        8.835 +- 2.295
    96 L      0.994**       9.192 +- 1.571



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  0.099  0.100  0.101  0.102  0.103  0.104
w2:   0.000  0.001  0.003  0.010  0.024  0.049  0.093  0.160  0.260  0.400

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.001 0.001 0.000 0.000 0.000
 0.004 0.002 0.001 0.001 0.000 0.000 0.000
 0.008 0.005 0.004 0.002 0.001 0.000 0.000 0.000 0.000
 0.016 0.010 0.008 0.005 0.003 0.002 0.001 0.000 0.000 0.000 0.000
 0.026 0.019 0.015 0.010 0.008 0.005 0.003 0.002 0.001 0.000 0.000 0.000 0.000
 0.041 0.031 0.026 0.018 0.015 0.010 0.007 0.004 0.003 0.002 0.001 0.000 0.000 0.000 0.000
 0.061 0.047 0.041 0.030 0.025 0.018 0.014 0.009 0.007 0.004 0.003 0.002 0.001 0.000 0.000 0.000 0.000
 0.086 0.068 0.060 0.046 0.040 0.029 0.025 0.017 0.014 0.009 0.007 0.004 0.003 0.001 0.001 0.000 0.000 0.000 0.000

sum of density on p0-p1 =   1.000000
