
seed used = 139991005

K12                                  ATG CTG GCG CTG ATG GAT GCG GAT GGA AAC ATT GCG TGG AGC GGG GAG TAT GAT GAG TGG GGC AAC CAG CTG AAT GAA GAG AAC CCG CAT CAC CTG CAC CAG CCG TAC CGG CTG CCG GGG CAG CAG TAT GAT AAG GAG TCG GGG CTG TAC TAC AAC CGG AAC CGG TAC TAC GAT CCG TTG CAG GGG CGG TAT ATC ACT CAG GAC CCG ATA GGG CTG GAG GGG GGA TGG AGT CTG TAT GCG TAT CCG CTG AAT CCG GTG AAT GGT ATT GAT CCA TTA GGG TTA AGT CCC GCA GAT GTA GCG CTA ATA AGA AGA AAA GAT CAA CTA AAC CAT CAA AGA GCA TGG GAT ATA TTA TCT GAT ACT TAT GAA GAT ATG AAG AGA TTA AAT TTA GGT GGG ACT GAT CAA TTT TTC CAT TGT ATG GCA TTT TGT CGA GTG TCT AAA TTA AAT GAC GCT GGT GTT AGC CGA TCG GCG AAA GGG CTG GGT TAT GAA AAA GAG ATT AGA GAT TAC GGG TTA AAT CTG TTC GGT ATG TAC GGC AGA AAA GTA AAG CTA TCC CAT TCT GAA ATG ATT GAA GAT AAT AAA AAA GAC TTG GCT GTA AAT GAC CAT GGG TTG ACA TGT CCA TCA ACA ACA GAT TGC TCA GAT AGA TGT AGT GAT TAT ATT AAT CCA GAG CAT AAA AAA ACG ATA AAG GCT TTA CAA GAT GCT GGC TAT CTC AAG 
O157                                 CCG CTG GCG CTC ATC AGC GAA GAC GGC AAT ACG GCG TGG AGC GGG GAG TAT GAT GAA TGG GGC AAC CAG CTG AAT GAG GAG AAC CCG CAT CAC CTG CAC CAG CCG TAC CGG CTG CCG GGG CAG CAG TAT GAT AAG GAG TCG GGG CTG TAC TAC AAC CGG AAC CGG TAC TAC GAT CCG TTG CAG GGG CGG TAT ATC ACT CAG GAC CCG ATA GGG CTG GAG GGG GGA TGG AGT CTG TAT GCG TAT CCG CTG AAT CCG GTG AAT GGT ATT GAT CCA TTA GGG TTA AGT CCC GCA GAT GTA GCG CTA ATA AGA AGA AAA GAT CAA CTA AAC CAT CAA AGA GCA TGG GAT ATA TTA TCT GAT ACT TAT GAA GAT ATG AAG AGA TTA AAT TTA GGT GGG ACT GAT CAA TTT TTC CAT TGT ATG GCA TTT TGT CGA GTG TCT AAA TTA AAT GAC GCT GGT GTT AGC CGA TCG GCG AAA GGG CTG GGT TAT GAA AAA GAG ATT AGA GAT TAC GGG TTA AAT CTG TTC GGT ATG TAC GGC AGA AAA GTA AAG CTA TCC CAT TCT GAA ATG ATT GAA GAT AAT AAA AAA GAC TTG GCT GTA AAT GAC CAT GGG TTG ACA TGT CCA TCA ACA ACA GAT TGC TCA GAT AGA TGT AGT GAT TAT ATT AAT CCA GAG CAT AAA GAA ACG ATA AAG GCT TTA CAA GAT GCT GGC TAT CTC AAG 
EDL933                               CCG CTG GCG CTC ATC AGC GAA GAC GGC AAT ACG GCG TGG AGC GGG GAG TAT GAT GAA TGG GGC AAC CAG CTG AAT GAG GAG AAC CCG CAT CAC CTG CAC CAG CCG TAC CGG CTG CCG GGG CAG CAG TAT GAT AAG GAG TCG GGG CTG TAC TAC AAC CGG AAC CGG TAC TAC GAT CCG TTG CAG GGG CGG TAT ATC ACT CAG GAC CCG ATA GGG CTG GAG GGG GGA TGG AGT CTG TAT GCG TAT CCG CTG AAT CCG GTG AAT GGT ATT GAT CCA TTA GGG TTA AGT CCC GCA GAT GTA GCG CTA ATA AGA AGA AAA GAT CAA CTA AAC CAT CAA AGA GCA TGG GAT ATA TTA TCT GAT ACT TAT GAA GAT ATG AAG AGA TTA AAT TTA GGT GGG ACT GAT CAA TTT TTC CAT TGT ATG GCA TTT TGT CGA GTG TCT AAA TTA AAT GAC GCT GGT GTT AGC CGA TCG GCG AAA GGG CTG GGT TAT GAA AAA GAG ATT AGA GAT TAC GGG TTA AAT CTG TTC GGT ATG TAC GGC AGA AAA GTA AAG CTA TCC CAT TCT GAA ATG ATT GAA GAT AAT AAA AAA GAC TTG GCT GTA AAT GAC CAT GGG TTG ACA TGT CCA TCA ACA ACA GAT TGC TCA GAT AGA TGT AGT GAT TAT ATT AAT CCA GAG CAT AAA GAA ACG ATA AAG GCT TTA CAA GAT GCT GGC TAT CTC AAG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0499.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 236
# site patterns = 65
    1   10    5    1    1    1    1    1    1    1    1    4    2   11    6
    9   16    1    3    5    6    9    1    7    6    2    7    4    5    2
    3    1    3    4    4    1    3    2    5    4    3    8    1    3    3
    3    7    8    4    3    4    4    2    2    4    2    4    1    1    3
    2    1    1    1    1

1       
K12                   ATG CTG GCG CTG ATG GAT GCG GAT GGA AAC ATT TGG AGC GGG GAG TAT GAT GAG GGC AAC CAG AAT GAA CCG CAT CAC TAC CGG AAG TCG TTG ATC ACT GAC ATA GGA AGT GTG GGT ATT CCA TTA CCC GCA GTA CTA AGA AAA CAA TCT GAA ATG TTT TTC TGT CGA GCT GTT TCC ACA TCA TGC AAA ACG CTC 
O157                  CC. ... ... ..C ..C AGC .AA ..C ..C ..T .CG ... ... ... ... ... ... ..A ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... 
EDL933                CC. ... ... ..C ..C AGC .AA ..C ..C ..T .CG ... ... ... ... ... ... ..A ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... 

Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT  2  2  2 | Ser TCT  3  3  3 | Tyr TAT  9  9  9 | Cys TGT  4  4  4
    TTC  2  2  2 |     TCC  1  1  1 |     TAC  7  7  7 |     TGC  1  1  1
Leu TTA  8  8  8 |     TCA  2  2  2 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  3  3  3 |     TCG  2  2  2 |     TAG  0  0  0 | Trp TGG  4  4  4
--------------------------------------------------------------------------
Leu CTT  0  0  0 | Pro CCT  0  0  0 | His CAT  6  6  6 | Arg CGT  0  0  0
    CTC  1  2  2 |     CCC  1  1  1 |     CAC  2  2  2 |     CGC  0  0  0
    CTA  3  3  3 |     CCA  3  3  3 | Gln CAA  4  4  4 |     CGA  2  2  2
    CTG 11 10 10 |     CCG  7  8  8 |     CAG  6  6  6 |     CGG  4  4  4
--------------------------------------------------------------------------
Ile ATT  5  4  4 | Thr ACT  3  3  3 | Asn AAT  9 10 10 | Ser AGT  3  3  3
    ATC  1  2  2 |     ACC  0  0  0 |     AAC  6  5  5 |     AGC  2  3  3
    ATA  4  4  4 |     ACA  3  3  3 | Lys AAA  9  8  8 | Arg AGA  7  7  7
Met ATG  6  4  4 |     ACG  1  2  2 |     AAG  5  5  5 |     AGG  0  0  0
--------------------------------------------------------------------------
Val GTT  1  1  1 | Ala GCT  4  4  4 | Asp GAT 18 16 16 | Gly GGT  5  5  5
    GTC  0  0  0 |     GCC  0  0  0 |     GAC  4  5  5 |     GGC  3  4  4
    GTA  3  3  3 |     GCA  3  3  3 | Glu GAA  5  7  7 |     GGA  2  1  1
    GTG  2  2  2 |     GCG  6  5  5 |     GAG  7  7  7 |     GGG 11 11 11
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.20339    C:0.21186    A:0.27119    G:0.31356
position  2:    T:0.22034    C:0.16525    A:0.41102    G:0.20339
position  3:    T:0.30508    C:0.13136    A:0.24576    G:0.31780

#2: O157           
position  1:    T:0.20339    C:0.21610    A:0.26695    G:0.31356
position  2:    T:0.21186    C:0.16949    A:0.41102    G:0.20763
position  3:    T:0.29661    C:0.14831    A:0.24576    G:0.30932

#3: EDL933         
position  1:    T:0.20339    C:0.21610    A:0.26695    G:0.31356
position  2:    T:0.21186    C:0.16949    A:0.41102    G:0.20763
position  3:    T:0.29661    C:0.14831    A:0.24576    G:0.30932

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       6 | Ser S TCT       9 | Tyr Y TAT      27 | Cys C TGT      12
      TTC       6 |       TCC       3 |       TAC      21 |       TGC       3
Leu L TTA      24 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG       9 |       TCG       6 |       TAG       0 | Trp W TGG      12
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       0 | His H CAT      18 | Arg R CGT       0
      CTC       5 |       CCC       3 |       CAC       6 |       CGC       0
      CTA       9 |       CCA       9 | Gln Q CAA      12 |       CGA       6
      CTG      31 |       CCG      23 |       CAG      18 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      13 | Thr T ACT       9 | Asn N AAT      29 | Ser S AGT       9
      ATC       5 |       ACC       0 |       AAC      16 |       AGC       8
      ATA      12 |       ACA       9 | Lys K AAA      25 | Arg R AGA      21
Met M ATG      14 |       ACG       5 |       AAG      15 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       3 | Ala A GCT      12 | Asp D GAT      50 | Gly G GGT      15
      GTC       0 |       GCC       0 |       GAC      14 |       GGC      11
      GTA       9 |       GCA       9 | Glu E GAA      19 |       GGA       4
      GTG       6 |       GCG      16 |       GAG      21 |       GGG      33
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.20339    C:0.21469    A:0.26836    G:0.31356
position  2:    T:0.21469    C:0.16808    A:0.41102    G:0.20621
position  3:    T:0.29944    C:0.14266    A:0.24576    G:0.31215

Codon frequencies under model, for use in evolver:
  0.01386456  0.00660529  0.01137940  0.01445315
  0.01085449  0.00517124  0.00890888  0.01131530
  0.02654334  0.01264565  0.00000000  0.00000000
  0.01331728  0.00634455  0.00000000  0.01388263
  0.01463481  0.00697225  0.01201159  0.01525610
  0.01145752  0.00545854  0.00940381  0.01194392
  0.02801797  0.01334818  0.02299588  0.02920741
  0.01405712  0.00669703  0.01153745  0.01465389
  0.01829352  0.00871531  0.01501449  0.01907013
  0.01432190  0.00682317  0.01175477  0.01492990
  0.03502246  0.01668523  0.02874485  0.03650926
  0.01757141  0.00837128  0.01442181  0.01831736
  0.02137453  0.01018315  0.01754325  0.02228194
  0.01673401  0.00797233  0.01373452  0.01744441
  0.04092098  0.01949537  0.03358609  0.04265819
  0.02053080  0.00978118  0.01685075  0.02140239



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                 
O157                 0.2811 (0.0156 0.0556)
EDL933               0.2811 (0.0156 0.0556)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 12
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1018.923740     +0.000000
   4..1     4..5     5..2     5..3  
  1.21099  0.80292  0.00000  0.00000  1.43980  0.97997  0.00000  0.06619 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   2.01392

(1: 1.210992, (2: 0.000004, 3: 0.000004): 0.802923);

(K12: 1.210992, (O157: 0.000004, EDL933: 0.000004): 0.802923);

Detailed output identifying parameters

kappa (ts/tv) =  1.43980


dN/dS for site classes (K=3)

p:   0.97997  0.00000  0.02003
w:   0.06619  1.00000999.00000

dN & dS for each branch

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

   4..1       1.211    151.6    556.4  20.0753   0.5068   0.0252    3.8  282.0
   4..5       0.803    151.6    556.4  20.0753   0.3360   0.0167    2.5  187.0
   5..2       0.000    151.6    556.4  20.0753   0.0000   0.0000    0.0    0.0
   5..3       0.000    151.6    556.4  20.0753   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      0.998**       996.857
     6 D      1.000**       998.924
     7 A      0.944         943.008
    11 I      0.983*        982.497


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

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

     1 M      0.932         7.911 +- 2.750
     5 M      0.530         4.715 +- 4.212
     6 D      0.947         8.026 +- 2.622
     7 A      0.609         5.390 +- 4.196
    11 I      0.866         7.419 +- 3.257



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:   0.699  0.220  0.060  0.015  0.004  0.001  0.000  0.000  0.000  0.000
w2:   0.012  0.017  0.025  0.039  0.059  0.086  0.120  0.162  0.212  0.269

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 0.001 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.017
 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 0.011 0.061
 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 0.045 0.189
 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 0.003 0.014 0.167 0.471

sum of density on p0-p1 =   1.000000
