
seed used = 139999301

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1460.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 378
# site patterns = 77
   10   18    6   20    4    1    7   20    6   10    1   18    2    8    4
    6    6    2    1    7    2    2    8    2    2    1    5   13    2    6
    9    1    7    5    1    1    9   12    5   10    3    3    7    1    2
    4    3    8    6    5    4    7    4    7    6    5    1    4    2    1
    2    1    1    5    5    4    3    2    1    1    3    1    2    1    1
    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 10 10 10 | Ser TCT  6  6  6 | Tyr TAT  5  6  6 | Cys TGT  2  2  2
    TTC  5  5  5 |     TCC  3  3  3 |     TAC  3  2  2 |     TGC  6  6  6
Leu TTA  7  8  8 |     TCA  4  5  5 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  4  4  4 |     TCG  2  2  2 |     TAG  0  0  0 | Trp TGG  6  6  6
--------------------------------------------------------------------------
Leu CTT  7  6  6 | Pro CCT  3  4  4 | His CAT  9  7  7 | Arg CGT  4  4  4
    CTC  2  2  2 |     CCC  2  0  0 |     CAC  7  9  9 |     CGC  2  2  2
    CTA  2  2  2 |     CCA  2  2  2 | Gln CAA  4  4  4 |     CGA  2  2  2
    CTG  8  8  8 |     CCG  1  1  1 |     CAG  4  4  4 |     CGG  4  4  4
--------------------------------------------------------------------------
Ile ATT 20 20 20 | Thr ACT  2  2  2 | Asn AAT 10 11 11 | Ser AGT  8  8  8
    ATC 10 10 10 |     ACC  2  2  2 |     AAC  5  5  5 |     AGC  1  1  1
    ATA  6  6  6 |     ACA  5  5  5 | Lys AAA 20 21 21 | Arg AGA  8  9  9
Met ATG 12 10 10 |     ACG  6  5  5 |     AAG 13 12 12 |     AGG  1  1  1
--------------------------------------------------------------------------
Val GTT  4  3  3 | Ala GCT  3  3  3 | Asp GAT 20 19 19 | Gly GGT  5  5  5
    GTC  7  8  8 |     GCC  6  6  6 |     GAC  8  8  8 |     GGC  2  2  2
    GTA  4  4  4 |     GCA 13 13 13 | Glu GAA 18 19 19 |     GGA  8  6  6
    GTG  3  5  5 |     GCG  6  6  6 |     GAG  9 10 10 |     GGG  7  7  7
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.16667    C:0.16667    A:0.34127    G:0.32540
position  2:    T:0.29365    C:0.17460    A:0.35714    G:0.17460
position  3:    T:0.31217    C:0.18783    A:0.27249    G:0.22751

#2: O157           
position  1:    T:0.17196    C:0.16138    A:0.33862    G:0.32804
position  2:    T:0.29365    C:0.17196    A:0.36243    G:0.17196
position  3:    T:0.30688    C:0.18783    A:0.28042    G:0.22487

#3: EDL933         
position  1:    T:0.17196    C:0.16138    A:0.33862    G:0.32804
position  2:    T:0.29365    C:0.17196    A:0.36243    G:0.17196
position  3:    T:0.30688    C:0.18783    A:0.28042    G:0.22487

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      30 | Ser S TCT      18 | Tyr Y TAT      17 | Cys C TGT       6
      TTC      15 |       TCC       9 |       TAC       7 |       TGC      18
Leu L TTA      23 |       TCA      14 | *** * TAA       0 | *** * TGA       0
      TTG      12 |       TCG       6 |       TAG       0 | Trp W TGG      18
------------------------------------------------------------------------------
Leu L CTT      19 | Pro P CCT      11 | His H CAT      23 | Arg R CGT      12
      CTC       6 |       CCC       2 |       CAC      25 |       CGC       6
      CTA       6 |       CCA       6 | Gln Q CAA      12 |       CGA       6
      CTG      24 |       CCG       3 |       CAG      12 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      60 | Thr T ACT       6 | Asn N AAT      32 | Ser S AGT      24
      ATC      30 |       ACC       6 |       AAC      15 |       AGC       3
      ATA      18 |       ACA      15 | Lys K AAA      62 | Arg R AGA      26
Met M ATG      32 |       ACG      16 |       AAG      37 |       AGG       3
------------------------------------------------------------------------------
Val V GTT      10 | Ala A GCT       9 | Asp D GAT      58 | Gly G GGT      15
      GTC      23 |       GCC      18 |       GAC      24 |       GGC       6
      GTA      12 |       GCA      39 | Glu E GAA      56 |       GGA      20
      GTG      13 |       GCG      18 |       GAG      29 |       GGG      21
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.17019    C:0.16314    A:0.33951    G:0.32716
position  2:    T:0.29365    C:0.17284    A:0.36067    G:0.17284
position  3:    T:0.30864    C:0.18783    A:0.27778    G:0.22575

Codon frequencies under model, for use in evolver:
  0.01605251  0.00976910  0.01444726  0.01174127
  0.00944833  0.00574998  0.00850349  0.00691078
  0.01971615  0.01199869  0.00000000  0.00000000
  0.00944833  0.00574998  0.00000000  0.00691078
  0.01538712  0.00936416  0.01384841  0.01125458
  0.00905669  0.00551164  0.00815102  0.00662432
  0.01889890  0.01150133  0.01700901  0.01382320
  0.00905669  0.00551164  0.00815102  0.00662432
  0.03202185  0.01948758  0.02881967  0.02342170
  0.01884770  0.01147017  0.01696293  0.01378574
  0.03933014  0.02393520  0.03539713  0.02876719
  0.01884770  0.01147017  0.01696293  0.01378574
  0.03085742  0.01877895  0.02777168  0.02257000
  0.01816233  0.01105307  0.01634609  0.01328444
  0.03789996  0.02306483  0.03410996  0.02772111
  0.01816233  0.01105307  0.01634609  0.01328444



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                 0.3643 (0.0136 0.0374)
EDL933               0.3643 (0.0136 0.0374)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 19
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1620.517048     +0.000000
   4..1     4..5     5..2     5..3  
  0.02027  0.08146  0.00000  0.00000 16.68555  0.99500  0.00000  0.52124 225.12396
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.10174

(1: 0.020272, (2: 0.000004, 3: 0.000004): 0.081457);

(K12: 0.020272, (O157: 0.000004, EDL933: 0.000004): 0.081457);

Detailed output identifying parameters

kappa (ts/tv) = 16.68555


dN/dS for site classes (K=3)

p:   0.99500  0.00000  0.00500
w:   0.52124  1.00000225.12396

dN & dS for each branch

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

   4..1       0.020    353.7    780.3   1.6451   0.0077   0.0047    1.7    6.0
   4..5       0.081    353.7    780.3   1.6451   0.0309   0.0188    6.7   24.1
   5..2       0.000    353.7    780.3   1.6451   0.0000   0.0000    0.0    0.0
   5..3       0.000    353.7    780.3   1.6451   0.0000   0.0000    0.0    0.0


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

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

   277 L      0.999**       224.950


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

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

   277 L      0.840         6.037 +- 3.393



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:   0.211  0.192  0.166  0.135  0.103  0.073  0.050  0.033  0.022  0.015
w2:   0.100  0.076  0.074  0.078  0.085  0.094  0.105  0.117  0.129  0.141

Posterior for p0-p1 (see the ternary graph)

 0.008
 0.001 0.004 0.012
 0.001 0.001 0.002 0.007 0.019
 0.000 0.000 0.001 0.001 0.003 0.011 0.029
 0.000 0.000 0.000 0.001 0.001 0.002 0.005 0.018 0.042
 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.004 0.007 0.028 0.056
 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.003 0.006 0.011 0.042 0.068
 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.003 0.004 0.008 0.016 0.058 0.074
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.003 0.004 0.006 0.012 0.024 0.074 0.073
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.003 0.003 0.005 0.008 0.017 0.033 0.085 0.067

sum of density on p0-p1 =   1.000000
