
seed used = 139995933

K12                                  ATG AAA CTT TTA AAA GTA GCA GCA ATT GCA GCA ATC GTA TTC TCC GGT AGC GCT CTG GCA GGT GTT GTT CCT CAG TAC GGC GGC GGC GGT --- AAC CAC GGT GGT GGC GGT AAT AAT AGC GGC CCA AAT TCT GAG CTG AAC ATT TAC CAG TAC GGT GGC GGT AAC TCT GCA CTT GCT CTG CAA ACT GAT GCC CGT AAC TCT GAC TTG ACT ATT ACC CAG CAT GGC GGC GGT AAT GGT GCA GAT GTT GGT CAG GGC TCA GAT GAC AGC TCA ATC GAT CTG ACC CAA CGT GGC TTC GGT AAC AGC GCT ACT CTT GAT CAG TGG AAC GGC AAA AAT TCT GAA ATG ACG GTT AAA CAG TTC GGT GGT GGC AAC GGT GCT GCA GTT GAC CAG ACT GCA TCT AAC TCC TCC GTC AAC GTG ACT CAG GTT GGC TTT GGT AAC AAC GCG ACC GCT CAT CAG TAC 
CFT073                               ATG AAA CTT TTA AAA GTA GCA GCA ATT GCA GCA ATC GTA TTC TCC GGT AGC GCT CTG GCA GGT GTT GTT CCT CAG TAC GGC GGC GGC GGT GGC AAC CAC GGT GGT GGC GGT AAT AAC AGC GGT CCG AAT TCA GAG CTG AAT ATT TAC CAG TAC GGT GGC GGT AAC TCT GCT CTT GCT CAG CAA GCT GAC GCC CGT AAC TCT GAT CTG ACC ATT ACC CAG CAC GGC GGC GGT AAT GGC GCA GAT GTG GGC CAA GGT TCT GAT GAC AGC TCA ATC GAT CTG ACT CAG CGT GGT TTC GGC AAC AGC GCT ACT CTT GAT CAG TGG AAT GGT AAA GAT TCT ACT ATG ACT GTT AAA CAG TTC GGT GGC GGT AAC GGT GCT GCT GTT GAC CAG ACT GCA TCT AAC TCC AGC GTT AAC GTC ACT CAG GTT GGC TTT GGT AAC AAC GCG ACC GCT CAT CAG TAC 
O157                                 ATG AAA CTT TTA AAA GTA GCA GCA ATT GCA GCA ATC GTA TTC TCC GGT AGC GCT CTG GCA GGT GTT GTT CCT CAG TAC GGC GGC GGT GGC GGT AAC CAC GGT GGT GGC GGT AAT AAC AGC GGC CCG AAT TCA GAG CTG AAT ATT TAT CAG TAC GGT GGT GGT AAC TCT GCA CTT GCT CTG CAA GCT GAT GCT CGT AAC TCT GAT CTT ACT ATT ACC CAG CAT GGT GGT GGT AAC GGT GCA GAT GTT GGT CAG GGC TCA GAT GAC AGC TCA ATC GAT CTG ACC CAA CGT GGC TTT GGT AAC AGC GCC ACT CTT GAT CAG TGG AAC GGT AAA GAC TCT CAT ATG ACA GTT AAA CAA TTC GGT GGC GGC AAC GGT GCA GCG GTT GAC CAG ACT GCA TCT AAT TCC ACC GTC AAC GTA ACT CAG GTT GGC TTT GGT AAC AAC GCG ACC GCT CAT CAG TAC 
EDL933                               ATG AAA CTT TTA AAA GTA GCA GCA ATT GCA GCA ATC GTA TTC TCC GGT AGC GCT CTG GCA GGT GTT GTT CCT CAG TAC GGC GGC GGT GGC GGT AAC CAC GGT GGT GGC GGT AAT AAC AGC GGC CCG AAT TCA GAG CTG AAT ATT TAT CAG TAC GGT GGT GGT AAC TCT GCA CTT GCT CTG CAA GCT GAT GCT CGT AAC TCT GAT CTT ACT ATT ACC CAG CAT GGT GGT GGT AAC GGT GCA GAT GTT GGT CAG GGC TCA GAT GAC AGC TCA ATC GAT CTG ACC CAA CGT GGC TTT GGT AAC AGC GCC ACT CTT GAT CAG TGG AAC GGT AAA GAC TCT CAT ATG ACA GTT AAA CAA TTC GGT GGC GGC AAC GGT GCA GCG GTT GAC CAG ACT GCA TCT AAT TCC ACC GTC AAC GTA ACT CAG GTT GGC TTT GGT AAC AAC GCG ACC GCT CAT CAG TAC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1042.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 152
# site patterns = 75
    2    4    3    1    2    7    3    2    2    2   11    4    3    3    5
    1    7    3    4    4    1    1    8    1    2    1    4    1    1    1
    1    1    4    1    1    1    1    1    1    2    1    1    1    2    1
    1    3    4    1    1    1    2    1    1    1    1    1    3    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1


K12                                  ATG AAA CTT TTA GTA GCA ATT ATC TTC TCC GGT AGC GCT CTG GTT CCT CAG TAC GGC GGC GGT --- AAC CAC AAT AAT GGC CCA TCT GAG AAC TAC TCT GCA CTG CAA ACT GAT GCC CGT GAC TTG ACT ACC CAT AAT GGT GAT GTT CAG TCA GAC TCA ACC CAA TTC GCT ACT TGG AAC GGC AAT GAA ACG CAG GGT GCT GCA AAC TCC GTC GTG TTT GCG CAT 
CFT073                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... GGC ... ... ... ..C ..T ..G ..A ... ..T ... ... ..T .A. ... G.. ..C ... ... ..T C.. ..C ... ..C ... ..C ... ..G ..A ..T ... ... ..T ..G ... ... ... ... ..T ..T G.. ACT ..T ... ..C ... ..T ... AG. ..T ..C ... ... ... 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..C GGT ... ... ... ..C ... ..G ..A ... ..T ..T ... ... ... ... G.. ... ..T ... ..T C.T ... ... ... ..C ... ... ... ... ... ... ... ... ... ..T ..C ... ... ... ..T G.C C.T ..A ..A ..C ..A ..G ..T A.. ... ..A ... ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..C GGT ... ... ... ..C ... ..G ..A ... ..T ..T ... ... ... ... G.. ... ..T ... ..T C.T ... ... ... ..C ... ... ... ... ... ... ... ... ... ..T ..C ... ... ... ..T G.C C.T ..A ..A ..C ..A ..G ..T A.. ... ..A ... ... ... 



Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT  1  1  2  2 | Ser TCT  5  5  4  4 | Tyr TAT  0  0  1  1 | Cys TGT  0  0  0  0
    TTC  3  3  2  2 |     TCC  3  2  2  2 |     TAC  4  4  3  3 |     TGC  0  0  0  0
Leu TTA  1  1  1  1 |     TCA  2  2  3  3 | *** TAA  0  0  0  0 | *** TGA  0  0  0  0
    TTG  1  0  0  0 |     TCG  0  0  0  0 |     TAG  0  0  0  0 | Trp TGG  1  1  1  1
--------------------------------------------------------------------------------------
Leu CTT  3  3  4  4 | Pro CCT  1  1  1  1 | His CAT  2  1  3  3 | Arg CGT  2  2  2  2
    CTC  0  0  0  0 |     CCC  0  0  0  0 |     CAC  1  2  1  1 |     CGC  0  0  0  0
    CTA  0  0  0  0 |     CCA  1  0  0  0 | Gln CAA  2  2  3  3 |     CGA  0  0  0  0
    CTG  4  4  4  4 |     CCG  0  1  1  1 |     CAG  9 10  8  8 |     CGG  0  0  0  0
--------------------------------------------------------------------------------------
Ile ATT  3  3  3  3 | Thr ACT  5  6  4  4 | Asn AAT  5  5  4  4 | Ser AGT  0  0  0  0
    ATC  2  2  2  2 |     ACC  3  3  4  4 |     AAC 11 10 11 11 |     AGC  4  5  4  4
    ATA  0  0  0  0 |     ACA  0  0  1  1 | Lys AAA  4  4  4  4 | Arg AGA  0  0  0  0
Met ATG  2  2  2  2 |     ACG  1  0  0  0 |     AAG  0  0  0  0 |     AGG  0  0  0  0
--------------------------------------------------------------------------------------
Val GTT  6  6  6  6 | Ala GCT  5  8  5  5 | Asp GAT  5  6  6  6 | Gly GGT 16 17 20 20
    GTC  1  1  1  1 |     GCC  1  1  1  1 |     GAC  3  3  3  3 |     GGC 13 13 10 10
    GTA  2  2  3  3 |     GCA  9  7  9  9 | Glu GAA  1  0  0  0 |     GGA  0  0  0  0
    GTG  1  1  0  0 |     GCG  1  1  2  2 |     GAG  1  1  1  1 |     GGG  0  0  0  0
--------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13907    C:0.16556    A:0.26490    G:0.43046
position  2:    T:0.19868    C:0.24503    A:0.31788    G:0.23841
position  3:    T:0.39073    C:0.32450    A:0.14570    G:0.13907

#2: CFT073         
position  1:    T:0.12500    C:0.17105    A:0.26316    G:0.44079
position  2:    T:0.19079    C:0.24342    A:0.31579    G:0.25000
position  3:    T:0.42105    C:0.32237    A:0.11842    G:0.13816

#3: O157           
position  1:    T:0.12500    C:0.17763    A:0.25658    G:0.44079
position  2:    T:0.19737    C:0.24342    A:0.31579    G:0.24342
position  3:    T:0.42763    C:0.28947    A:0.15789    G:0.12500

#4: EDL933         
position  1:    T:0.12500    C:0.17763    A:0.25658    G:0.44079
position  2:    T:0.19737    C:0.24342    A:0.31579    G:0.24342
position  3:    T:0.42763    C:0.28947    A:0.15789    G:0.12500

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       6 | Ser S TCT      18 | Tyr Y TAT       2 | Cys C TGT       0
      TTC      10 |       TCC       9 |       TAC      14 |       TGC       0
Leu L TTA       4 |       TCA      10 | *** * TAA       0 | *** * TGA       0
      TTG       1 |       TCG       0 |       TAG       0 | Trp W TGG       4
------------------------------------------------------------------------------
Leu L CTT      14 | Pro P CCT       4 | His H CAT       9 | Arg R CGT       8
      CTC       0 |       CCC       0 |       CAC       5 |       CGC       0
      CTA       0 |       CCA       1 | Gln Q CAA      10 |       CGA       0
      CTG      16 |       CCG       3 |       CAG      35 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      12 | Thr T ACT      19 | Asn N AAT      18 | Ser S AGT       0
      ATC       8 |       ACC      14 |       AAC      43 |       AGC      17
      ATA       0 |       ACA       2 | Lys K AAA      16 | Arg R AGA       0
Met M ATG       8 |       ACG       1 |       AAG       0 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      24 | Ala A GCT      23 | Asp D GAT      23 | Gly G GGT      73
      GTC       4 |       GCC       4 |       GAC      12 |       GGC      46
      GTA      10 |       GCA      34 | Glu E GAA       1 |       GGA       0
      GTG       2 |       GCG       6 |       GAG       4 |       GGG       0
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.12850    C:0.17298    A:0.26030    G:0.43822
position  2:    T:0.19605    C:0.24382    A:0.31631    G:0.24382
position  3:    T:0.41680    C:0.30643    A:0.14498    G:0.13180

Codon frequencies under model, for use in evolver:
  0.01066864  0.00784335  0.00371083  0.00337348
  0.01326856  0.00975475  0.00461515  0.00419559
  0.01721327  0.01265481  0.00000000  0.00000000
  0.01326856  0.00975475  0.00000000  0.00419559
  0.01436163  0.01055835  0.00499535  0.00454123
  0.01786153  0.01313140  0.00621270  0.00564791
  0.02317171  0.01703533  0.00805972  0.00732702
  0.01786153  0.01313140  0.00621270  0.00564791
  0.02161084  0.01588781  0.00751681  0.00683347
  0.02687734  0.01975963  0.00934864  0.00849876
  0.03486790  0.02563411  0.01212797  0.01102542
  0.02687734  0.01975963  0.00934864  0.00849876
  0.03638280  0.02674783  0.01265489  0.01150444
  0.04524920  0.03326621  0.01573885  0.01430805
  0.05870166  0.04315616  0.02041797  0.01856179
  0.04524920  0.03326621  0.01573885  0.01430805



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

K12                 
CFT073               0.0691 (0.0223 0.3235)
O157                 0.0678 (0.0178 0.2631) 0.0275 (0.0118 0.4280)
EDL933               0.0678 (0.0178 0.2631) 0.0275 (0.0118 0.4280)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  6  np: 11):   -805.782831     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
  0.09780  0.03919  0.29285  0.19874  0.00000  0.00000  3.83780  0.98037  0.00000  0.01394 10.80260
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.62858

(1: 0.097797, (2: 0.292846, (3: 0.000004, 4: 0.000004): 0.198741): 0.039192);

(K12: 0.097797, (CFT073: 0.292846, (O157: 0.000004, EDL933: 0.000004): 0.198741): 0.039192);

Detailed output identifying parameters

kappa (ts/tv) =  3.83780


dN/dS for site classes (K=3)

p:   0.98037  0.00000  0.01963
w:   0.01394  1.00000 10.80260

dN & dS for each branch

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

   5..1       0.098    130.1    325.9   0.2257   0.0165   0.0730    9.5    5.4
   5..6       0.039    130.1    325.9   0.2257   0.0066   0.0293    3.8    2.2
   6..2       0.293    130.1    325.9   0.2257   0.0493   0.2186   28.4   16.1
   6..7       0.199    130.1    325.9   0.2257   0.0335   0.1484   19.3   10.9
   7..3       0.000    130.1    325.9   0.2257   0.0000   0.0000    0.0    0.0
   7..4       0.000    130.1    325.9   0.2257   0.0000   0.0000    0.0    0.0


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

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

    60 L      0.685         7.403
   113 E      1.000**       10.803
   135 S      0.998**       10.781


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

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

   113 E      0.980*        7.418 +- 2.455
   135 S      0.862         6.683 +- 3.134



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:   1.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.012  0.028  0.050  0.075  0.099  0.120  0.138  0.151  0.160  0.166

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 0.000
 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 0.000
 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 0.000 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 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.996

sum of density on p0-p1 =   1.000000
