
seed used = 140011533

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2650.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 160
# site patterns = 77
    4    7    1    1   11    3    5    3    3    5    2    3    1    3    3
    4    9   12    4    2    3    2    1    5    1    3    3    1    1    1
    2    1    3    1    1    1    1    2    1    1    1    1    3    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1

1       
K12                   ATG TTA GTT AGT AAA AGC AAC GGA TTT GCT GCA GTT TTG GGT AGT TAT AAT GAA TCT CAC GAG CTA CAT ATT TTA TGT AAG TCA ACG CGC CTT ACT CAA ATG ATA GGC GCC GTC GGA CGT GAA GGT GTA TTC AAT CAC GAG AGT TCT CCT GAC ATA CAG TGG CTC CTA AAG CTG GAA AAC AAT GTG TTT ACT AAA TTA TCG AAT AAT GCC GAT CAG TTT TTT TGC GCT AGA 
O157                  ... ... A.. .A. ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... .T. ... ..A ... ... ... ... ..G ... ..T .A. ... ... G.. G.A .T. .C. GA. ... ... G.. ... ... ... T.. ..A .C. ..G .T. ..G ... GC. GT. C.T .C. G.. GG. G.G ATT ..G ..A ..A G.. ..G T.. ... 
EDL933                ... ... A.. .A. ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... .T. ... ..A ... ... ... ... ..G ... ..T .A. ... ... G.. G.A .T. .C. GA. ... ... G.. ... ... ... T.. ..A .C. ..G .T. ..G ... GC. GT. C.T .C. G.. GG. G.G ATT ..G ..A ..A G.. ..G T.. ... 

Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT  6  3  3 | Ser TCT  5  5  5 | Tyr TAT  4  4  4 | Cys TGT  3  3  3
    TTC  1  1  1 |     TCC  0  0  0 |     TAC  0  0  0 |     TGC  1  0  0
Leu TTA  9  9  9 |     TCA  1  2  2 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  1  0  0 |     TCG  1  0  0 |     TAG  0  0  0 | Trp TGG  1  3  3
--------------------------------------------------------------------------
Leu CTT  2  2  2 | Pro CCT  1  1  1 | His CAT  1  2  2 | Arg CGT  1  1  1
    CTC  1  1  1 |     CCC  0  0  0 |     CAC  3  2  2 |     CGC  1  1  1
    CTA  3  2  2 |     CCA  0  0  0 | Gln CAA  3  4  4 |     CGA  0  0  0
    CTG  1  0  0 |     CCG  0  1  1 |     CAG  2  1  1 |     CGG  0  0  0
--------------------------------------------------------------------------
Ile ATT  5  8  8 | Thr ACT  2  1  1 | Asn AAT 13 10 10 | Ser AGT  5  3  3
    ATC  0  1  1 |     ACC  0  0  0 |     AAC  6  5  5 |     AGC  3  3  3
    ATA  2  2  2 |     ACA  0  0  0 | Lys AAA 12 12 12 | Arg AGA  1  1  1
Met ATG  5  4  4 |     ACG  1  1  1 |     AAG  4  4  4 |     AGG  0  0  0
--------------------------------------------------------------------------
Val GTT  4  5  5 | Ala GCT  6  6  6 | Asp GAT  1  4  4 | Gly GGT  4  4  4
    GTC  2  2  2 |     GCC  2  1  1 |     GAC  1  1  1 |     GGC  1  1  1
    GTA  3  5  5 |     GCA  2  2  2 | Glu GAA 14 13 13 |     GGA  4  3  3
    GTG  1  2  2 |     GCG  0  1  1 |     GAG  4  6  6 |     GGG  0  1  1
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.20625    C:0.11875    A:0.36875    G:0.30625
position  2:    T:0.28750    C:0.13125    A:0.42500    G:0.15625
position  3:    T:0.39375    C:0.13750    A:0.33750    G:0.13125

#2: O157           
position  1:    T:0.18750    C:0.11250    A:0.34375    G:0.35625
position  2:    T:0.29375    C:0.13125    A:0.42500    G:0.15000
position  3:    T:0.38750    C:0.11875    A:0.34375    G:0.15000

#3: EDL933         
position  1:    T:0.18750    C:0.11250    A:0.34375    G:0.35625
position  2:    T:0.29375    C:0.13125    A:0.42500    G:0.15000
position  3:    T:0.38750    C:0.11875    A:0.34375    G:0.15000

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      12 | Ser S TCT      15 | Tyr Y TAT      12 | Cys C TGT       9
      TTC       3 |       TCC       0 |       TAC       0 |       TGC       1
Leu L TTA      27 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG       1 |       TCG       1 |       TAG       0 | Trp W TGG       7
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       3 | His H CAT       5 | Arg R CGT       3
      CTC       3 |       CCC       0 |       CAC       7 |       CGC       3
      CTA       7 |       CCA       0 | Gln Q CAA      11 |       CGA       0
      CTG       1 |       CCG       2 |       CAG       4 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      21 | Thr T ACT       4 | Asn N AAT      33 | Ser S AGT      11
      ATC       2 |       ACC       0 |       AAC      16 |       AGC       9
      ATA       6 |       ACA       0 | Lys K AAA      36 | Arg R AGA       3
Met M ATG      13 |       ACG       3 |       AAG      12 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      14 | Ala A GCT      18 | Asp D GAT       9 | Gly G GGT      12
      GTC       6 |       GCC       4 |       GAC       3 |       GGC       3
      GTA      13 |       GCA       6 | Glu E GAA      40 |       GGA      10
      GTG       5 |       GCG       2 |       GAG      16 |       GGG       2
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.19375    C:0.11458    A:0.35208    G:0.33958
position  2:    T:0.29167    C:0.13125    A:0.42500    G:0.15208
position  3:    T:0.38958    C:0.12500    A:0.34167    G:0.14375

Codon frequencies under model, for use in evolver:
  0.02317517  0.00743588  0.02032475  0.00855127
  0.01042883  0.00334615  0.00914614  0.00384807
  0.03376953  0.01083514  0.00000000  0.00000000
  0.01208420  0.00387728  0.00000000  0.00445887
  0.01370575  0.00439757  0.01202001  0.00505720
  0.00616759  0.00197890  0.00540901  0.00227574
  0.01997123  0.00640788  0.01751488  0.00736906
  0.00714657  0.00229302  0.00626758  0.00263697
  0.04211402  0.01351252  0.03693422  0.01553940
  0.01895131  0.00608063  0.01662040  0.00699273
  0.06136614  0.01968967  0.05381843  0.02264312
  0.02195945  0.00704581  0.01925856  0.00810269
  0.04061885  0.01303279  0.03562295  0.01498770
  0.01827848  0.00586475  0.01603033  0.00674447
  0.05918746  0.01899063  0.05190772  0.02183922
  0.02117983  0.00679567  0.01857482  0.00781502



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                 1.6602 (0.1066 0.0642)
EDL933               1.6602 (0.1066 0.0642)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 35
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -790.128070     +0.000000
   4..1     4..5     5..2     5..3  
  0.35190  0.06518  0.00000  0.00000  2.97268  0.69217  0.00000  0.00000  7.84573
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.41709

(1: 0.351900, (2: 0.000004, 3: 0.000004): 0.065179);

(K12: 0.351900, (O157: 0.000004, EDL933: 0.000004): 0.065179);

Detailed output identifying parameters

kappa (ts/tv) =  2.97268


dN/dS for site classes (K=3)

p:   0.69217  0.00000  0.30783
w:   0.00000  1.00000  7.84573

dN & dS for each branch

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

   4..1       0.352    101.3    378.7   2.4152   0.1338   0.0554    5.6   50.7
   4..5       0.065    101.3    378.7   2.4152   0.0248   0.0103    1.0    9.4
   5..2       0.000    101.3    378.7   2.4152   0.0000   0.0000    0.0    0.0
   5..3       0.000    101.3    378.7   2.4152   0.0000   0.0000    0.0    0.0


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

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

     3 V      1.000**       7.846
     4 S      1.000**       7.846
    15 L      1.000**       7.846
    37 L      1.000**       7.846
    55 T      1.000**       7.846
    59 M      1.000**       7.846
    86 E      1.000**       7.846
    88 G      1.000**       7.846
   100 N      1.000**       7.846
   103 H      1.000**       7.846
   104 E      1.000**       7.846
   107 S      1.000**       7.846
   108 S      1.000**       7.846
   114 I      1.000**       7.846
   130 L      1.000**       7.846
   132 N      1.000**       7.846
   133 N      1.000**       7.846
   137 F      1.000**       7.846
   140 T      1.000**       7.846
   141 K      1.000**       7.846
   143 L      1.000**       7.846
   144 S      1.000**       7.846
   147 N      1.000**       7.846
   148 N      1.000**       7.846
   149 A      1.000**       7.846
   150 D      1.000**       7.846
   152 F      1.000**       7.846
   153 F      1.000**       7.846
   155 C      1.000**       7.846
   156 A      1.000**       7.846


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

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

     3 V      0.551         4.813 +- 3.890
    15 L      0.732         6.252 +- 3.656
    37 L      0.668         5.744 +- 3.800
    55 T      0.559         4.872 +- 3.889
    59 M      0.544         4.750 +- 3.884
    86 E      0.520         4.581 +- 3.889
    88 G      0.508         4.477 +- 3.871
   103 H      0.942         7.852 +- 2.496
   104 E      0.681         5.844 +- 3.778
   107 S      0.633         5.458 +- 3.848
   108 S      0.945         7.872 +- 2.472
   114 I      0.566         4.934 +- 3.890
   130 L      0.741         6.320 +- 3.631
   132 N      0.680         5.839 +- 3.780
   133 N      0.562         4.909 +- 3.896
   137 F      0.935         7.792 +- 2.564
   140 T      0.911         7.604 +- 2.756
   141 K      0.927         7.736 +- 2.625
   143 L      0.683         5.857 +- 3.773
   144 S      0.730         6.239 +- 3.661
   147 N      0.881         7.377 +- 2.956
   148 N      0.901         7.529 +- 2.828
   149 A      0.933         7.779 +- 2.579
   150 D      0.562         4.902 +- 3.896
   152 F      0.635         5.481 +- 3.846
   153 F      0.641         5.531 +- 3.841
   155 C      0.730         6.236 +- 3.661
   156 A      0.639         5.514 +- 3.844



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:   0.175  0.159  0.141  0.122  0.103  0.086  0.071  0.058  0.047  0.039
w2:   0.000  0.005  0.017  0.041  0.075  0.113  0.150  0.181  0.203  0.216

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.014 0.002 0.000
 0.008 0.017 0.017 0.002 0.000
 0.001 0.005 0.013 0.023 0.020 0.002 0.000
 0.000 0.001 0.002 0.009 0.019 0.029 0.021 0.001 0.000
 0.000 0.000 0.001 0.002 0.004 0.015 0.029 0.034 0.021 0.001 0.000
 0.000 0.000 0.000 0.001 0.001 0.003 0.008 0.023 0.039 0.036 0.019 0.001 0.000
 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.006 0.013 0.034 0.049 0.036 0.017 0.001 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.003 0.010 0.020 0.045 0.056 0.033 0.015 0.001 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.006 0.016 0.030 0.054 0.058 0.030 0.013 0.001 0.000

sum of density on p0-p1 =   1.000000
