
seed used = 139989301

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0282.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 194
# site patterns = 105
    1    1    1    1    1    1    1    1    1    1    2    1    1    1    3
    4    2    3    4    3    3    1    4    1    1    3    1    1    1    2
    2    1    2    1    3    2    1    1    2    2    1    1    2    1    1
    1    2    1    1    1    1    1    1    1    1    1    3    1    1    3
    3    3    5    1    3    1    2    1    4    3    4    3    6    1    1
    1    1    4    3    5    6    1    3    2    2    6    1    2    2    2
    2    1    1    1    1    1    1    1    2    1    1    1    1    1    1


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



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

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

#1: K12            
position  1:    T:0.16912    C:0.30882    A:0.22059    G:0.30147
position  2:    T:0.30147    C:0.24265    A:0.25000    G:0.20588
position  3:    T:0.30147    C:0.25000    A:0.16912    G:0.27941

#2: O157           
position  1:    T:0.13918    C:0.27835    A:0.22165    G:0.36082
position  2:    T:0.30928    C:0.26289    A:0.26289    G:0.16495
position  3:    T:0.35052    C:0.22680    A:0.17526    G:0.24742

#3: EDL933         
position  1:    T:0.13918    C:0.27835    A:0.22165    G:0.36082
position  2:    T:0.30928    C:0.26289    A:0.26289    G:0.16495
position  3:    T:0.35052    C:0.22680    A:0.17526    G:0.24742

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      12 | Ser S TCT       4 | Tyr Y TAT      14 | Cys C TGT       3
      TTC      14 |       TCC       6 |       TAC       3 |       TGC       1
Leu L TTA       0 |       TCA       2 | *** * TAA       0 | *** * TGA       0
      TTG       6 |       TCG       3 |       TAG       0 | Trp W TGG       9
------------------------------------------------------------------------------
Leu L CTT      24 | Pro P CCT       6 | His H CAT       5 | Arg R CGT      14
      CTC       8 |       CCC       5 |       CAC       2 |       CGC       9
      CTA       2 |       CCA      15 | Gln Q CAA       6 |       CGA       0
      CTG      19 |       CCG      15 |       CAG      17 |       CGG       3
------------------------------------------------------------------------------
Ile I ATT      24 | Thr T ACT      10 | Asn N AAT      11 | Ser S AGT       0
      ATC       8 |       ACC       3 |       AAC       5 |       AGC       5
      ATA       3 |       ACA       5 | Lys K AAA       3 | Arg R AGA       3
Met M ATG       8 |       ACG       7 |       AAG      11 |       AGG      10
------------------------------------------------------------------------------
Val V GTT      13 | Ala A GCT      16 | Asp D GAT      14 | Gly G GGT       7
      GTC       9 |       GCC      20 |       GAC      11 |       GGC      13
      GTA       5 |       GCA      11 | Glu E GAA      26 |       GGA      10
      GTG       6 |       GCG       7 |       GAG       8 |       GGG       5
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.14695    C:0.28626    A:0.22137    G:0.34542
position  2:    T:0.30725    C:0.25763    A:0.25954    G:0.17557
position  3:    T:0.33779    C:0.23282    A:0.17366    G:0.25573

Codon frequencies under model, for use in evolver:
  0.01557578  0.01073585  0.00800789  0.01179183
  0.01306044  0.00900211  0.00671469  0.00988756
  0.01315718  0.00906879  0.00000000  0.00000000
  0.00890045  0.00613477  0.00000000  0.00673819
  0.03034243  0.02091399  0.01559978  0.02297111
  0.02544241  0.01753658  0.01308056  0.01926149
  0.02563087  0.01766648  0.01317745  0.01940416
  0.01733853  0.01195085  0.00891416  0.01312635
  0.02346481  0.01617349  0.01206383  0.01776432
  0.01967546  0.01356162  0.01011563  0.01489555
  0.01982121  0.01366208  0.01019056  0.01500589
  0.01340846  0.00924199  0.00689362  0.01015104
  0.03661320  0.02523622  0.01882374  0.02771847
  0.03070051  0.02116080  0.01578388  0.02324219
  0.03092792  0.02131755  0.01590080  0.02341436
  0.02092183  0.01442070  0.01075642  0.01583912



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                 0.4634 (0.0890 0.1921)
EDL933               0.4634 (0.0890 0.1921)-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):   -947.423446     +0.000000
   4..1     4..5     5..2     5..3  
  3.58138  3.80284  0.00000  0.00000  2.03684  0.90230  0.00000  0.25191 336.10101
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   7.38423

(1: 3.581384, (2: 0.000004, 3: 0.000004): 3.802835);

(K12: 3.581384, (O157: 0.000004, EDL933: 0.000004): 3.802835);

Detailed output identifying parameters

kappa (ts/tv) =  2.03684


dN/dS for site classes (K=3)

p:   0.90230  0.00000  0.09770
w:   0.25191  1.00000336.10101

dN & dS for each branch

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

   4..1       3.581    166.4    415.6  33.0633   1.6518   0.0500    8.3  686.5
   4..5       3.803    166.4    415.6  33.0633   1.7539   0.0530    8.8  728.9
   5..2       0.000    166.4    415.6  33.0633   0.0000   0.0000    0.0    0.0
   5..3       0.000    166.4    415.6  33.0633   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      0.938         315.422
     2 P      0.892         299.734
     3 A      0.832         279.696
     5 V      0.918         308.508
     7 L      0.998**       335.291
     8 I      1.000**       335.985
    12 G      0.921         309.688
    13 R      0.957*        321.810
    71 G      0.999**       335.814
    72 G      0.929         312.197
    73 N      0.951*        319.770
    82 T      0.867         291.565


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

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

     1 M      0.814         7.333 +- 3.484
     2 P      0.593         5.482 +- 4.203
     3 A      0.592         5.470 +- 4.198
     5 V      0.630         5.800 +- 4.153
     6 V      0.523         4.882 +- 4.224
     7 L      0.931         8.291 +- 2.589
     8 I      0.984*        8.706 +- 1.940
    12 G      0.704         6.427 +- 3.985
    13 R      0.910         8.118 +- 2.782
    66 C      0.624         5.742 +- 4.154
    67 F      0.519         4.849 +- 4.226
    70 S      0.612         5.642 +- 4.173
    71 G      0.981*        8.684 +- 1.981
    72 G      0.824         7.416 +- 3.442
    73 N      0.820         7.389 +- 3.461
    82 T      0.596         5.511 +- 4.203
   185 Y      0.549         5.099 +- 4.219



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:   0.389  0.268  0.163  0.090  0.046  0.023  0.011  0.005  0.003  0.001
w2:   0.001  0.002  0.008  0.021  0.043  0.076  0.120  0.175  0.239  0.314

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.001 0.001
 0.000 0.000 0.001 0.002 0.002
 0.000 0.000 0.000 0.000 0.002 0.005 0.003
 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.011 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.016 0.019 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.012 0.040 0.029 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.034 0.082 0.036 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 0.015 0.076 0.134 0.036 0.003
 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 0.009 0.039 0.139 0.174 0.032 0.003

sum of density on p0-p1 =   1.000000
