
seed used = 140013569

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2851.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 163
# site patterns = 61
    3    1    2    9    8    2    4   11    4    8    1   10    5    4    8
    1    3    1    1    1    3    3    1    1    1    2    2    1   13    4
    4    3    1    1    1    1    1    2    1    1    1    3    1    4    2
    1    1    1    1    2    1    1    1    1    2    1    1    1    1    1
    1

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

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

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

#1: K12            
position  1:    T:0.23926    C:0.15337    A:0.31902    G:0.28834
position  2:    T:0.23926    C:0.14724    A:0.49693    G:0.11656
position  3:    T:0.39877    C:0.15951    A:0.31902    G:0.12270

#2: O157           
position  1:    T:0.24540    C:0.14724    A:0.30675    G:0.30061
position  2:    T:0.23313    C:0.16564    A:0.48466    G:0.11656
position  3:    T:0.40491    C:0.14110    A:0.33129    G:0.12270

#3: EDL933         
position  1:    T:0.24540    C:0.14724    A:0.30675    G:0.30061
position  2:    T:0.23313    C:0.16564    A:0.48466    G:0.11656
position  3:    T:0.40491    C:0.14110    A:0.33129    G:0.12270

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       3 | Ser S TCT       0 | Tyr Y TAT      39 | Cys C TGT      12
      TTC      14 |       TCC       2 |       TAC      12 |       TGC       3
Leu L TTA      12 |       TCA      11 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG       3 |       TAG       0 | Trp W TGG       3
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       3 | His H CAT      11 | Arg R CGT       3
      CTC       3 |       CCC       1 |       CAC       4 |       CGC       0
      CTA      12 |       CCA       0 | Gln Q CAA      17 |       CGA       0
      CTG       3 |       CCG       3 |       CAG       7 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      24 | Thr T ACT       3 | Asn N AAT      33 | Ser S AGT      12
      ATC       6 |       ACC       2 |       AAC       7 |       AGC       1
      ATA       7 |       ACA       6 | Lys K AAA      25 | Arg R AGA       3
Met M ATG       9 |       ACG       3 |       AAG      11 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       6 | Ala A GCT       5 | Asp D GAT      26 | Gly G GGT      11
      GTC       0 |       GCC       0 |       GAC      14 |       GGC       3
      GTA       5 |       GCA      30 | Glu E GAA      29 |       GGA       3
      GTG       0 |       GCG       6 |       GAG       4 |       GGG       3
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.24335    C:0.14928    A:0.31084    G:0.29652
position  2:    T:0.23517    C:0.15951    A:0.48875    G:0.11656
position  3:    T:0.40286    C:0.14724    A:0.32720    G:0.12270

Codon frequencies under model, for use in evolver:
  0.02460076  0.00899114  0.01998031  0.00749262
  0.01668573  0.00609834  0.01355186  0.00508195
  0.05112680  0.01868594  0.00000000  0.00000000
  0.01219342  0.00445648  0.00000000  0.00371373
  0.01509122  0.00551557  0.01225683  0.00459631
  0.01023579  0.00374100  0.00831333  0.00311750
  0.03136350  0.01146280  0.02547289  0.00955233
  0.00748000  0.00273381  0.00607512  0.00227817
  0.03142282  0.01148448  0.02552107  0.00957040
  0.02131287  0.00778948  0.01730995  0.00649123
  0.06530482  0.02386775  0.05303945  0.01988979
  0.01557479  0.00569231  0.01264958  0.00474359
  0.02997572  0.01095559  0.02434576  0.00912966
  0.02033136  0.00743075  0.01651278  0.00619229
  0.06229736  0.02276858  0.05059684  0.01897382
  0.01485753  0.00543016  0.01206703  0.00452514



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                 0.3597 (0.0233 0.0648)
EDL933               0.3597 (0.0233 0.0648)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 13
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -694.890659     +0.000000
   4..1     4..5     5..2     5..3  
  0.90254  0.00000  0.00000  0.00000 56.22074  0.94594  0.00000  0.07062 204.72036
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.90255

(1: 0.902544, (2: 0.000004, 3: 0.000004): 0.000000);

(K12: 0.902544, (O157: 0.000004, EDL933: 0.000004): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) = 56.22074


dN/dS for site classes (K=3)

p:   0.94594  0.00000  0.05406
w:   0.07062  1.00000204.72036

dN & dS for each branch

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

   4..1       0.903    143.0    346.0  11.1338   0.4100   0.0368    5.3  141.8
   4..5       0.000    143.0    346.0  11.1338   0.0000   0.0000    0.0    0.0
   5..2       0.000    143.0    346.0  11.1338   0.0000   0.0000    0.0    0.0
   5..3       0.000    143.0    346.0  11.1338   0.0000   0.0000    0.0    0.0


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

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

     2 S      1.000**       204.643
    56 I      0.730         149.476
    65 F      0.965*        197.525
    79 D      0.571         116.842
    86 P      0.999**       204.503
   104 F      0.935         191.367
   142 D      0.974*        199.423
   156 N      0.982*        201.011


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

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

     2 S      0.798         5.686 +- 3.478
   104 F      0.500         3.774 +- 3.617



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:   0.212  0.177  0.146  0.119  0.096  0.076  0.060  0.047  0.037  0.029
w2:   0.097  0.080  0.078  0.081  0.087  0.094  0.104  0.114  0.126  0.139

Posterior for p0-p1 (see the ternary graph)

 0.011
 0.004 0.010 0.014
 0.001 0.003 0.005 0.013 0.019
 0.001 0.001 0.002 0.004 0.008 0.018 0.023
 0.001 0.001 0.001 0.002 0.003 0.006 0.011 0.024 0.028
 0.000 0.001 0.001 0.001 0.002 0.002 0.004 0.008 0.016 0.032 0.032
 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.005 0.012 0.023 0.040 0.034
 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.005 0.008 0.018 0.032 0.048 0.033
 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.004 0.006 0.011 0.025 0.045 0.054 0.031
 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.002 0.004 0.005 0.009 0.015 0.036 0.060 0.058 0.028

sum of density on p0-p1 =   1.000000
