
seed used = 139998961

K12                                  ATG AAA AAA GAG AAC TAT TCA TTC AAG CAA GCT TGT GCT GTT GTC GGT GGG CAA TCA GCA ATG GCT AGG CTT TTA GGT GTA TCA CCT CCA AGC GTA AAT CAA TGG ATC AAA GGG GTA CGT CAA TTG CCT GCC GAG AGA TGT CCA GCA ATT GAA CGT GCA ACA AGA GGT GAG GTT CTG TGC GAA GAA CTT CGT CCT GAT ATT GAC TGG TCA TAT TTA CGA CGT TCG GCA TGT TGT TCG CAG AAT ATG TCA GTG AAG CAA CTA AAT GAC AGT AAC --- --- --- --- --- --- AAA TCC TCA TTT GAT CAT ACC 
O157                                 ATG AAA AAA GAT AAC TAT TCA TTC AAA CGA GCT TGT GCT GTT GTC GGT GGG CAA TCA GCA ATG GCT AGG CTT TTA GGT GTA TCT CCT CCA AGC GTA AAT CAA TGG ATC AAA GGT GTA CGT CAG TTG CCT GCT GAG AGA TGT CCT GCG ATT GAA CGA GCA ACA AAA GGT GGT GTC CTG TGT GAA GAA CTT CGT CCT GAT GTT GAT TGG ACA TAC TTA CGA CGC TCG TCA TGT TAT TCG CAG AAT ATG TCG ATG AAG CAA CCA AAT GAC GAA AAC GAT CAT ACC CGA AGC ATC AAG AGG CAA ATG ATT CAT GAA 
EDL933                               ATG AAA AAA GAT AAC TAT TCA TTC AAA CGA GCT TGT GCT GTT GTC GGT GGG CAA TCA GCA ATG GCT AGG CTT TTA GGT GTA TCT CCT CCA AGC GTA AAT CAA TGG ATC AAA GGT GTA CGT CAG TTG CCT GCT GAG AGA TGT CCT GCG ATT GAA CGA GCA ACA AAA GGT GGT GTC CTG TGT GAA GAA CTT CGT CCT GAT GTT GAT TGG ACA TAC TTA CGA CGC TCG TCA TGT TAT TCG CAG AAT ATG TCG ATG AAG CAA CCA AAT GAC GAA AAC GAT CAT ACC CGA AGC ATC AAG AGG CAA ATG ATT CAT GAA 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1357.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 104
# site patterns = 76
    3    3    1    2    1    2    1    1    1    3    3    1    1    3    1
    3    2    1    2    2    3    1    3    1    1    3    2    1    1    2
    1    1    1    1    1    1    1    1    3    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    2    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1

K12                                  ATG AAA GAG AAC TAT TCA TTC AAG CAA GCT TGT GTT GTC GGT GGG CAA GCA AGG CTT TTA GTA TCA CCT CCA AGC AAT TGG ATC GGG CGT CAA TTG GCC GAG AGA CCA GCA ATT GAA CGT ACA AGA GAG GTT CTG TGC GAT ATT GAC TCA TAT CGA CGT TCG GCA TGT CAG TCA GTG AAG CTA GAC AGT --- --- --- --- --- --- AAA TCC TCA TTT GAT CAT ACC 
O157                                 ... ... ..T ... ... ... ... ..A .G. ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ..T ... ..G ... ..T ... ... ..T ..G ... ... ..A ... .A. .GT ..C ... ..T ... G.. ..T A.. ..C ... ..C ... T.. .A. ... ..G A.. ... .C. ... GAA GAT CAT ACC CGA AGC ATC ..G AGG CA. A.G AT. ... GAA 
EDL933                               ... ... ..T ... ... ... ... ..A .G. ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ..T ... ..G ... ..T ... ... ..T ..G ... ... ..A ... .A. .GT ..C ... ..T ... G.. ..T A.. ..C ... ..C ... T.. .A. ... ..G A.. ... .C. ... GAA GAT CAT ACC CGA AGC ATC ..G AGG CA. A.G AT. ... GAA 



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

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

#1: K12            
position  1:    T:0.23469    C:0.21429    A:0.24490    G:0.30612
position  2:    T:0.22449    C:0.24490    A:0.30612    G:0.22449
position  3:    T:0.33673    C:0.12245    A:0.34694    G:0.19388

#2: O157           
position  1:    T:0.19231    C:0.23077    A:0.27885    G:0.29808
position  2:    T:0.22115    C:0.22115    A:0.32692    G:0.23077
position  3:    T:0.35577    C:0.12500    A:0.31731    G:0.20192

#3: EDL933         
position  1:    T:0.19231    C:0.23077    A:0.27885    G:0.29808
position  2:    T:0.22115    C:0.22115    A:0.32692    G:0.23077
position  3:    T:0.35577    C:0.12500    A:0.31731    G:0.20192

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       1 | Ser S TCT       2 | Tyr Y TAT       6 | Cys C TGT      12
      TTC       3 |       TCC       1 |       TAC       2 |       TGC       1
Leu L TTA       6 |       TCA      12 | *** * TAA       0 | *** * TGA       0
      TTG       3 |       TCG       8 |       TAG       0 | Trp W TGG       6
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT      11 | His H CAT       5 | Arg R CGT       8
      CTC       0 |       CCC       0 |       CAC       0 |       CGC       2
      CTA       1 |       CCA       6 | Gln Q CAA      13 |       CGA       9
      CTG       3 |       CCG       0 |       CAG       5 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       6 | Thr T ACT       0 | Asn N AAT       9 | Ser S AGT       1
      ATC       5 |       ACC       3 |       AAC       6 |       AGC       5
      ATA       0 |       ACA       5 | Lys K AAA      14 | Arg R AGA       4
Met M ATG      13 |       ACG       0 |       AAG       6 |       AGG       5
------------------------------------------------------------------------------
Val V GTT       6 | Ala A GCT      11 | Asp D GAT      10 | Gly G GGT      13
      GTC       5 |       GCC       1 |       GAC       4 |       GGC       0
      GTA       9 |       GCA       8 | Glu E GAA      13 |       GGA       0
      GTG       1 |       GCG       2 |       GAG       5 |       GGG       4
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.20588    C:0.22549    A:0.26797    G:0.30065
position  2:    T:0.22222    C:0.22876    A:0.32026    G:0.22876
position  3:    T:0.34967    C:0.12418    A:0.32680    G:0.19935

Codon frequencies under model, for use in evolver:
  0.01684160  0.00598113  0.01573981  0.00960129
  0.01733694  0.00615704  0.01620275  0.00988368
  0.02427172  0.00861986  0.00000000  0.00000000
  0.01733694  0.00615704  0.00000000  0.00988368
  0.01844556  0.00655076  0.01723884  0.01051569
  0.01898808  0.00674343  0.01774587  0.01082498
  0.02658331  0.00944080  0.02484422  0.01515497
  0.01898808  0.00674343  0.01774587  0.01082498
  0.02192081  0.00778496  0.02048674  0.01249691
  0.02256554  0.00801393  0.02108929  0.01286447
  0.03159176  0.01121950  0.02952501  0.01801026
  0.02256554  0.00801393  0.02108929  0.01286447
  0.02459408  0.00873435  0.02298513  0.01402093
  0.02531744  0.00899124  0.02366116  0.01443331
  0.03544442  0.01258774  0.03312562  0.02020663
  0.02531744  0.00899124  0.02366116  0.01443331



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                 
O157                 0.3965 (0.1165 0.2939)
EDL933               0.3965 (0.1165 0.2939)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -559.288651     +0.000000
   4..1     4..5     5..2     5..3  
 15.19942  0.00000  0.00000  0.00000  3.91552  0.69796  0.24483  0.00000 386.88529
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  15.19943

(1: 15.199421, (2: 0.000004, 3: 0.000004): 0.000000);

(K12: 15.199421, (O157: 0.000004, EDL933: 0.000004): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  3.91552


dN/dS for site classes (K=3)

p:   0.69796  0.24483  0.05721
w:   0.00000  1.00000386.88529

dN & dS for each branch

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

   4..1      15.199     77.4    234.6  22.3787   6.6397   0.2967   23.0 1557.8
   4..5       0.000     77.4    234.6  22.3787   0.0000   0.0000    0.0    0.0
   5..2       0.000     77.4    234.6  22.3787   0.0000   0.0000    0.0    0.0
   5..3       0.000     77.4    234.6  22.3787   0.0000   0.0000    0.0    0.0


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

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

    90 S      0.675         261.484
    99 S      0.992**       383.785
   100 S      0.574         222.587
   101 F      0.734         284.271
   104 T      0.924         357.728


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

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

    57 E      0.569         4.608 +- 3.800
    90 S      0.823         6.487 +- 3.282
    99 S      0.970*        7.559 +- 2.487
   100 S      0.827         6.530 +- 3.286
   101 F      0.782         6.211 +- 3.444
   102 D      0.701         5.596 +- 3.615
   104 T      0.912         7.150 +- 2.883



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:   0.679  0.272  0.044  0.004  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.005  0.022  0.047  0.071  0.094  0.114  0.133  0.152  0.171  0.190

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 0.001 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.012 0.021
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.026 0.065 0.048
 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 0.026 0.111 0.152 0.043
 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 0.003 0.019 0.093 0.197 0.147 0.020

sum of density on p0-p1 =   1.000000
