
seed used = 140016365

K12                                  ATG GAC TGG TAT CTG AAA GTA CTA AAA AAT TAT GTC GGT TTC CGG GGT CGT GCG CGG CGC AAA GAG TAC TGG ATG TTT ATT CTG GTC AAC ATC ATC TTT ACG TTC GTG CTG GGG CTG CTG GAT AAA ATG TTA GGC TGG CAA CGC GCT GGT GGC GAA GGC ATC CTG ACG ACA ATC TAC GGT ATT CTG GTG TTT TTA CCG TGG TGG GCG GTT CAG TTC CGC CGC CTG CAC GAC ACC GAC CGC TCG GCG TGG TGG GCA CTG CTA TTC TTA ATC CCG TTT ATC GGC TGG CTT ATT ATC ATC GTC TTT AAC TGC CAG GCG GGT ACG CCA GGC GAA AAC CGC TTT GGA CCA GAT CCA AAA CTG GAA CCT 
S2457T                               ATG GAC TGG TAT CTG AAA GTA CTA AAA AAT TAT GTC GGT TTC CGG GGT CGT GCG CGG CGC AAA GAG TAC TGG ATG TTT ATT CTG GTC AAC ATC ATC TTT ACG TTC GTG CTG GGG CTG CTG GAT AAA ATG TTA GGC TGG CAA CGC GCT GGT GGC GAA GGC ATC CTG ACG ATA ATC TAC GGT ATT CTG GTG TTT TTA CCG TGG TGG GCG GTT CAG TTC CGC CGC CTG CAC GAC ACC GAC CGC TCG GCG TGG TGG GCA CTG CTA TTC TTA ATC CCG TTT ATC GGC TGG CTT ATT ATC ATC GTC TTT AAC TGC CAG GCG GGT ACG CCA GGC GAA AAC CGC TTT GGA CCA GAT CCA AAA CTG GAA CAA 
Shig4337                             ATG GAC TGG TAT CTG AAA GTA CTA AAA AAT TAT GTC GGT TTC CGG GGT CGT GCG CGG CGC AAA GAG TAC TGG ATG TTT ATT CTG GTC AAC ATC ATC TTT ACG TTC GTG CTG GGG CTG CTG GAT AAA ATG TTA GGC TGG CAA CGC GCT GGT GGC GAA GGC ATC CTG ACG ATA ATC TAC GGT ATT CTG GTG TTT TTA CCG TGG TGG GCG GTT CAG TTC CGC CGC CTG CAC GAC ACC GAC CGC TCG GCG TGG TGG GCA CTG CTA TTC TTA ATC CCG TTT ATC GGC TGG CTT ATT ATC ATC GTC TTT AAC TGC CAG GCG GGT ACG CCA GGC GAA AAC CGC TTT GGA CCA GAT CCA AAA CTG GAA CAA 
CFT073                               ATG GAC TGG TAT CTG AAA GTA CTA AAA AAT TAT GTC GGT TTC CGG GGT CGT GCG CGG CGC AAA GAG TAC TGG ATG TTT ATT CTG GTC AAC ATC ATC TTT ACG TTC GTG CTG GGG CTA CTG GAT AAA ATG TTA GGC TGG CAA CGT GCC GGT GGC GAA GGC ATC CTG ACG ACA ATC TAC GGT ATT CTG GTG TTT TTA CCA TGG TGG GCA GTT CAG TTC CGC CGC CTG CAC GAC ACC GAC CGC TCG GCG TGG TGG GCA CTG CTA TTC TTA ATC CCG TTC ATC GGC TGG CTT ATT ATC ATC GTC TTT AAC TGC CAG GCG GGT ACG CCA GGC GAA AAC CGC TTT GGA CCA GAT CCG AAA CTG GAA CAA 
O157                                 ATG GAC TGG TAT CTG AAA GTA CTA AAA AAT TAT GTC GGT TTC CGG GGT CGT GCG CGG CGC AAA GAG TAC TGG ATG TTT ATT CTG GTC AAC ATC ATC TTT ACG TTC GTG CTG GGG CTG CTG GAT AAA ATG TTA GGC TGG CAA CGC GCT GGT GGC GAA GGC ATC CTG ACG ACA ATC TAC GGT ATT CTG GTG TTT TTA CCG TGG TGG GCA GTT CAG TTC CGC CGC CTG CAC GAC ACC GAC CGC TCG GCG TGG TGG GCA CTG CTA TTC TTA ATC CCG TTT ATC GGC TGG CTT ATT ATC ATC GTC TTT AAC TGC CAG GCG GGT ACG CCA GGC GAA AAC CGC TTT GGA CCT GAT CCA AAA CTG GAA CCT 
EDL933                               ATG GAC TGG TAT CTG AAA GTA CTA AAA AAT TAT GTC GGT TTC CGG GGT CGT GCG CGG CGC AAA GAG TAC TGG ATG TTT ATT CTG GTC AAC ATC ATC TTT ACG TTC GTG CTG GGG CTG CTG GAT AAA ATG TTA GGC TGG CAA CGC GCT GGT GGC GAA GGC ATC CTG ACG ACA ATC TAC GGT ATT CTG GTG TTT TTA CCG TGG TGG GCA GTT CAG TTC CGC CGC CTG CAC GAC ACC GAC CGC TCG GCG TGG TGG GCA CTG CTA TTC TTA ATC CCG TTT ATC GGC TGG CTT ATT ATC ATC GTC TTT AAC TGC CAG GCG GGT ACG CCA GGC GAA AAC CGC TTT GGA CCT GAT CCA AAA CTG GAA CCT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3103.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 121
# site patterns = 51
    3    3    8    2    9    5    1    2    1    3    5    4    2    1    3
    5    1    2    5    3    3    8    3    2    1    1    2    3    5    1
    1    1    3    1    1    1    1    2    1    1    1    1    1    1    1
    1    1    1    1    1    1

1       
K12                   ATG GAC TGG TAT CTG AAA GTA CTA AAT GTC GGT TTC CGG CGT GCG CGC GAG TAC TTT ATT AAC ATC ACG GTG GGG CTG GAT TTA GGC CAA CGC GCT GAA ACA CCG GCG GTT CAG CAC ACC TCG GCA CCG TTT CTT TGC CCA GGA CCA CCA CCT 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AA 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AA 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..T ..C ... ... ..A ..A ... ... ... ... ... ... ... ..C ... ... ... ... ... ..G .AA 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  6  6  6  5  6  6 | Ser TCT  0  0  0  0  0  0 | Tyr TAT  2  2  2  2  2  2 | Cys TGT  0  0  0  0  0  0
    TTC  4  4  4  5  4  4 |     TCC  0  0  0  0  0  0 |     TAC  2  2  2  2  2  2 |     TGC  1  1  1  1  1  1
Leu TTA  3  3  3  3  3  3 |     TCA  0  0  0  0  0  0 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  0  0  0  0  0  0 |     TCG  1  1  1  1  1  1 |     TAG  0  0  0  0  0  0 | Trp TGG  8  8  8  8  8  8
--------------------------------------------------------------------------------------------------------------
Leu CTT  1  1  1  1  1  1 | Pro CCT  1  0  0  0  2  2 | His CAT  0  0  0  0  0  0 | Arg CGT  1  1  1  2  1  1
    CTC  0  0  0  0  0  0 |     CCC  0  0  0  0  0  0 |     CAC  1  1  1  1  1  1 |     CGC  6  6  6  5  6  6
    CTA  2  2  2  3  2  2 |     CCA  3  3  3  3  2  2 | Gln CAA  1  2  2  2  1  1 |     CGA  0  0  0  0  0  0
    CTG 10 10 10  9 10 10 |     CCG  2  2  2  2  2  2 |     CAG  2  2  2  2  2  2 |     CGG  2  2  2  2  2  2
--------------------------------------------------------------------------------------------------------------
Ile ATT  3  3  3  3  3  3 | Thr ACT  0  0  0  0  0  0 | Asn AAT  1  1  1  1  1  1 | Ser AGT  0  0  0  0  0  0
    ATC  8  8  8  8  8  8 |     ACC  1  1  1  1  1  1 |     AAC  3  3  3  3  3  3 |     AGC  0  0  0  0  0  0
    ATA  0  1  1  0  0  0 |     ACA  1  0  0  1  1  1 | Lys AAA  5  5  5  5  5  5 | Arg AGA  0  0  0  0  0  0
Met ATG  3  3  3  3  3  3 |     ACG  3  3  3  3  3  3 |     AAG  0  0  0  0  0  0 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  1  1  1  1  1  1 | Ala GCT  1  1  1  0  1  1 | Asp GAT  2  2  2  2  2  2 | Gly GGT  5  5  5  5  5  5
    GTC  3  3  3  3  3  3 |     GCC  0  0  0  1  0  0 |     GAC  3  3  3  3  3  3 |     GGC  5  5  5  5  5  5
    GTA  1  1  1  1  1  1 |     GCA  1  1  1  2  2  2 | Glu GAA  3  3  3  3  3  3 |     GGA  1  1  1  1  1  1
    GTG  2  2  2  2  2  2 |     GCG  4  4  4  3  3  3 |     GAG  1  1  1  1  1  1 |     GGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.22314    C:0.26446    A:0.23140    G:0.28099
position  2:    T:0.38843    C:0.14876    A:0.21488    G:0.24793
position  3:    T:0.19835    C:0.30579    A:0.17355    G:0.32231

#2: S2457T         
position  1:    T:0.22314    C:0.26446    A:0.23140    G:0.28099
position  2:    T:0.39669    C:0.13223    A:0.22314    G:0.24793
position  3:    T:0.19008    C:0.30579    A:0.18182    G:0.32231

#3: Shig4337       
position  1:    T:0.22314    C:0.26446    A:0.23140    G:0.28099
position  2:    T:0.39669    C:0.13223    A:0.22314    G:0.24793
position  3:    T:0.19008    C:0.30579    A:0.18182    G:0.32231

#4: CFT073         
position  1:    T:0.22314    C:0.26446    A:0.23140    G:0.28099
position  2:    T:0.38843    C:0.14050    A:0.22314    G:0.24793
position  3:    T:0.18182    C:0.31405    A:0.19835    G:0.30579

#5: O157           
position  1:    T:0.22314    C:0.26446    A:0.23140    G:0.28099
position  2:    T:0.38843    C:0.14876    A:0.21488    G:0.24793
position  3:    T:0.20661    C:0.30579    A:0.17355    G:0.31405

#6: EDL933         
position  1:    T:0.22314    C:0.26446    A:0.23140    G:0.28099
position  2:    T:0.38843    C:0.14876    A:0.21488    G:0.24793
position  3:    T:0.20661    C:0.30579    A:0.17355    G:0.31405

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      35 | Ser S TCT       0 | Tyr Y TAT      12 | Cys C TGT       0
      TTC      25 |       TCC       0 |       TAC      12 |       TGC       6
Leu L TTA      18 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       6 |       TAG       0 | Trp W TGG      48
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       5 | His H CAT       0 | Arg R CGT       7
      CTC       0 |       CCC       0 |       CAC       6 |       CGC      35
      CTA      13 |       CCA      16 | Gln Q CAA       9 |       CGA       0
      CTG      59 |       CCG      12 |       CAG      12 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      18 | Thr T ACT       0 | Asn N AAT       6 | Ser S AGT       0
      ATC      48 |       ACC       6 |       AAC      18 |       AGC       0
      ATA       2 |       ACA       4 | Lys K AAA      30 | Arg R AGA       0
Met M ATG      18 |       ACG      18 |       AAG       0 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       6 | Ala A GCT       5 | Asp D GAT      12 | Gly G GGT      30
      GTC      18 |       GCC       1 |       GAC      18 |       GGC      30
      GTA       6 |       GCA       9 | Glu E GAA      18 |       GGA       6
      GTG      12 |       GCG      21 |       GAG       6 |       GGG       6
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.22314    C:0.26446    A:0.23140    G:0.28099
position  2:    T:0.39118    C:0.14187    A:0.21901    G:0.24793
position  3:    T:0.19559    C:0.30716    A:0.18044    G:0.31680

Codon frequencies under model, for use in evolver:
  0.01767917  0.02776377  0.01630966  0.02863528
  0.00641181  0.01006925  0.00591512  0.01038533
  0.00989785  0.01554380  0.00000000  0.00000000
  0.01120511  0.01759676  0.00000000  0.01814912
  0.02095309  0.03290521  0.01932997  0.03393811
  0.00759918  0.01193393  0.00701052  0.01230854
  0.01173078  0.01842228  0.01082206  0.01900056
  0.01328013  0.02085541  0.01225139  0.02151007
  0.01833396  0.02879206  0.01691372  0.02969584
  0.00664929  0.01044219  0.00613420  0.01076997
  0.01026443  0.01611950  0.00946930  0.01662549
  0.01162011  0.01824849  0.01071996  0.01882131
  0.02226266  0.03496178  0.02053809  0.03605924
  0.00807413  0.01267980  0.00744867  0.01307782
  0.01246395  0.01957367  0.01149844  0.02018810
  0.01411014  0.02215888  0.01301710  0.02285445



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               1.6166 (0.0092 0.0057)
Shig4337             1.6166 (0.0092 0.0057)-1.0000 (0.0000 0.0000)
CFT073               0.0612 (0.0055 0.0897) 0.0435 (0.0036 0.0839) 0.0435 (0.0036 0.0839)
O157                 0.0000 (0.0000 0.0228) 0.3184 (0.0092 0.0288) 0.3184 (0.0092 0.0288) 0.0612 (0.0055 0.0897)
EDL933               0.0000 (0.0000 0.0228) 0.3184 (0.0092 0.0288) 0.3184 (0.0092 0.0288) 0.0612 (0.0055 0.0897)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 11
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -557.717991     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00939  0.00000  0.04515  0.00000  0.00000  0.00284  0.17976  0.01253  0.00000  0.00000  3.88587  0.99164  0.00000  0.05438 131.74448
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.24969

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.045152): 0.009387, (4: 0.179758, (5: 0.000004, 6: 0.000004): 0.012534): 0.002838);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.045152): 0.009387, (CFT073: 0.179758, (O157: 0.000004, EDL933: 0.000004): 0.012534): 0.002838);

Detailed output identifying parameters

kappa (ts/tv) =  3.88587


dN/dS for site classes (K=3)

p:   0.99164  0.00000  0.00836
w:   0.05438  1.00000131.74448

dN & dS for each branch

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

   7..8       0.009    113.1    249.9   1.1548   0.0033   0.0028    0.3    0.8
   8..1       0.000    113.1    249.9   1.1548   0.0000   0.0000    0.0    0.0
   8..9       0.045    113.1    249.9   1.1548   0.0157   0.0136    1.5    3.9
   9..2       0.000    113.1    249.9   1.1548   0.0000   0.0000    0.0    0.0
   9..3       0.000    113.1    249.9   1.1548   0.0000   0.0000    0.0    0.0
   7..10      0.003    113.1    249.9   1.1548   0.0010   0.0009    0.1    0.2
  10..4       0.180    113.1    249.9   1.1548   0.0625   0.0541    6.1   15.6
  10..11      0.013    113.1    249.9   1.1548   0.0044   0.0038    0.4    1.1
  11..5       0.000    113.1    249.9   1.1548   0.0000   0.0000    0.0    0.0
  11..6       0.000    113.1    249.9   1.1548   0.0000   0.0000    0.0    0.0


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

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

   121 P      1.000**       131.744


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

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

    57 T      0.510         4.455 +- 4.146
   121 P      0.993**       8.131 +- 2.198



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:   0.743  0.195  0.047  0.011  0.003  0.001  0.000  0.000  0.000  0.000
w2:   0.008  0.016  0.029  0.048  0.071  0.098  0.129  0.163  0.200  0.239

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.011
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005 0.047
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.023 0.181
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.091 0.627

sum of density on p0-p1 =   1.000000
