
seed used = 140004633

K12                                  TTG TCT GGA GAT TCA GGG GGC CAG TCT AGT GGC GAA GCA TCC TCC CGT GTT TTA ATT CTC ATT GAT GGT CAG GAG GTA ACT TAT CAG CGC GCC GGA GAT AAT TAT GGT GTG GGA CTG TTG ATA GAT GAG TCT GCG CTG GAG CGT GTT GAG GTA GTG AAA GGT CCA TAT TCC GTA CTG TAC GGT TCA CAG GCA ATT GGC GGT ATT GTT AAC TTC ATC ACC AAA AAG GGT --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GAA TCT CCG GAC --- --- --- --- --- TCC CTA TAT CAC TTA AAT 
CFT073                               TTG GCA GGC CGT AAA CAA ATC CGC ATT CGT GGC GAA GCA TCC TCC CGT GTT TTA ATT CTC ATT GAT GGT CAG GAG GTA ACT TAT CAG CGC GCC GGA GAT AAT TAT GGT GTG GGA CTG TTG ATA GAT GAG TCT GCG CTG GAG CGT GTT GAG GTA GTG AAA GGT CCA TAT TCC GTA CTG TAC GGT TCA CAG GCA ATT GGC GGT ATT GTT AAC TTC ATA ACC AAA AAG GGA GGT GAC AAA CTT GCA TCT GGA GTT GTG AAA GCT GTT TAT AAT TCC GCA ACA GCA GGC TGG GAA GAA TCA ATC GCG GTC CAG GGG AGC ATC GGT GGA TTT GAT TAT CGC ATC AAC GGT AGT TAT TCT GAT CAG GGC AAT CGT GAT ACG CCG GAT GGA CGT CTG CCG AAT ACC AAC TAT CGT AAC AAT 
O157                                 TTG GCA GGC CGT AAA CAA ATC CGC ATT CGT GGC GAA GCA TCC TCC CGT GTT TTA ATT CTC ATT GAT GGT CAG GAG GTA ACT TAT CAG CGC GCC GGA GAT AAT TAT GGT GTG GGA CTG TTG ATA GAT GAG TCT GCG CTG GAG CGT GTT GAG GTA GTG AAA GGT CCA TAT TCC GTA CTG TAC GGT TCA CAG GCA ATT GGC GGT ATT GTT AAC TTC ATC ACC AAA AAG GGA GGT GAC AAA CTT GCA TCT GGA GTT GTG AAA GCT GTT TAT AAT TCC GCA ACA GCA GGC TGG GAA GAA TCA ATC GCG GTC CAG GGG AGC ATC GGT GGA TTT GAT TAT CGC ATC AAC GGT AGT TAT TCT GAT CAG GGC AAT CGT GAT ACG CCG GAT GGA CGT CTG CCG AAT ACC AAC TAT CGT AAC AAT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1998.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 138
# site patterns = 85
    2    1    1    1    1    1    1    1    1    1    2    1    2    3    2
    3    1    4    1    3    5    3    4    3    1    4    1    1    2    2
    2    3    1    1    1    2    1    1    1    1    1    1    1    1    1
    3    1    2    1    3    2    3    2    1    1    3    3    1    1    2
    1    2    1    3    1    1    2    1    1    1    2    1    1    1    2
    1    1    1    1    1    1    1    1    1    1

K12                                  TTG TCT GGA GAT TCA GGG GGC CAG TCT AGT GGC GAA GCA TCC CGT GTT TTA ATT CTC GAT GGT CAG GAG GTA ACT TAT CGC GCC GGA AAT GTG CTG ATA TCT GCG AAA CCA TAC TCA AAC TTC ATC ACC AAG GGT --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GAA TCT CCG GAC --- --- TCC CTA CAC TTA 
CFT073                               ... G.A ..C CG. AA. CAA AT. .GC AT. C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..A GGT GAC AAA CTT GCA TCT GGA GTT GTG GCT TAT AAT TCC ACA GGC TGG GAA TCA ATC GCG GTC CAG GGG AGC TTT GAT CGC AAC AGT CGT ..T A.G ... ..T CTG CCG A.. AAC .GT AAC 
O157                                 ... G.A ..C CG. AA. CAA AT. .GC AT. C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A GGT GAC AAA CTT GCA TCT GGA GTT GTG GCT TAT AAT TCC ACA GGC TGG GAA TCA ATC GCG GTC CAG GGG AGC TTT GAT CGC AAC AGT CGT ..T A.G ... ..T CTG CCG A.. AAC .GT AAC 



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

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

#1: K12            
position  1:    T:0.23256    C:0.17442    A:0.17442    G:0.41860
position  2:    T:0.27907    C:0.20930    A:0.31395    G:0.19767
position  3:    T:0.36047    C:0.19767    A:0.22093    G:0.22093

#2: CFT073         
position  1:    T:0.16667    C:0.18116    A:0.23913    G:0.41304
position  2:    T:0.24638    C:0.19565    A:0.31884    G:0.23913
position  3:    T:0.37681    C:0.21014    A:0.22464    G:0.18841

#3: O157           
position  1:    T:0.16667    C:0.18116    A:0.23913    G:0.41304
position  2:    T:0.24638    C:0.19565    A:0.31884    G:0.23913
position  3:    T:0.37681    C:0.21739    A:0.21739    G:0.18841

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       2 | Ser S TCT      10 | Tyr Y TAT      18 | Cys C TGT       0
      TTC       3 |       TCC      12 |       TAC       3 |       TGC       0
Leu L TTA       4 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG       6 |       TCG       0 |       TAG       0 | Trp W TGG       2
------------------------------------------------------------------------------
Leu L CTT       2 | Pro P CCT       0 | His H CAT       0 | Arg R CGT      16
      CTC       3 |       CCC       0 |       CAC       1 |       CGC       7
      CTA       1 |       CCA       3 | Gln Q CAA       2 |       CGA       0
      CTG      11 |       CCG       5 |       CAG      14 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      14 | Thr T ACT       3 | Asn N AAT      12 | Ser S AGT       3
      ATC      10 |       ACC       5 |       AAC       9 |       AGC       2
      ATA       4 |       ACA       2 | Lys K AAA      12 | Arg R AGA       0
Met M ATG       0 |       ACG       2 |       AAG       3 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      13 | Ala A GCT       2 | Asp D GAT      18 | Gly G GGT      22
      GTC       2 |       GCC       3 |       GAC       3 |       GGC      13
      GTA       9 |       GCA      14 | Glu E GAA       8 |       GGA      15
      GTG       8 |       GCG       5 |       GAG      12 |       GGG       3
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.18232    C:0.17956    A:0.22376    G:0.41436
position  2:    T:0.25414    C:0.19890    A:0.31768    G:0.22928
position  3:    T:0.37293    C:0.20994    A:0.22099    G:0.19613

Codon frequencies under model, for use in evolver:
  0.01787690  0.01006403  0.01059372  0.00940192
  0.01399061  0.00787620  0.00829073  0.00735803
  0.02234612  0.01258004  0.00000000  0.00000000
  0.01612807  0.00907951  0.00000000  0.00848217
  0.01760603  0.00991155  0.01043321  0.00925947
  0.01377864  0.00775686  0.00816512  0.00724654
  0.02200754  0.01238943  0.01304151  0.01157434
  0.01588370  0.00894194  0.00941257  0.00835365
  0.02193983  0.01235131  0.01300138  0.01153872
  0.01717030  0.00966624  0.01017499  0.00903031
  0.02742478  0.01543914  0.01625172  0.01442340
  0.01979354  0.01114303  0.01172950  0.01040994
  0.04062931  0.02287280  0.02407663  0.02136801
  0.03179685  0.01790045  0.01884258  0.01672279
  0.05078664  0.02859100  0.03009578  0.02671001
  0.03665470  0.02063524  0.02172131  0.01927766



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                 
CFT073               0.8556 (0.1299 0.1519)
O157                 0.9705 (0.1299 0.1339) 0.0000 (0.0000 0.0095)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -669.820596     +0.000000
   4..1     4..5     5..2     5..3  
  1.00302  0.46540  0.00784  0.00000  0.24854  0.84330  0.00000  0.07606 43.94783
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.47626

(1: 1.003015, (2: 0.007841, 3: 0.000004): 0.465403);

(K12: 1.003015, (CFT073: 0.007841, O157: 0.000004): 0.465403);

Detailed output identifying parameters

kappa (ts/tv) =  0.24854


dN/dS for site classes (K=3)

p:   0.84330  0.00000  0.15670
w:   0.07606  1.00000 43.94783

dN & dS for each branch

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

   4..1       1.003     82.6    331.4   6.9508   0.4032   0.0580    4.8  133.6
   4..5       0.465     82.6    331.4   6.9508   0.1871   0.0269    2.2   62.0
   5..2       0.008     82.6    331.4   6.9508   0.0032   0.0005    0.0    1.0
   5..3       0.000     82.6    331.4   6.9508   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      0.953*        41.905
     4 D      0.999**       43.916
     5 S      1.000**       43.930
     6 G      1.000**       43.947
     7 G      1.000**       43.936
     8 Q      0.997**       43.836
     9 S      1.000**       43.930
    10 S      0.641         28.195
   124 E      0.531         23.354
   125 S      0.972*        42.709
   133 S      0.817         35.915
   134 L      1.000**       43.947
   136 H      0.997**       43.814
   137 L      1.000**       43.947


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

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

     2 S      0.731         7.422 +- 4.171
     4 D      0.972*        9.652 +- 1.726
     5 S      0.977*        9.694 +- 1.621
     6 G      0.996**       9.869 +- 1.049
     7 G      0.980*        9.730 +- 1.523
     8 Q      0.956*        9.509 +- 2.054
     9 S      0.980*        9.723 +- 1.542
    10 S      0.631         6.478 +- 4.517
   125 S      0.765         7.737 +- 3.995
   133 S      0.764         7.721 +- 3.999
   134 L      0.994**       9.855 +- 1.106
   136 H      0.931         9.279 +- 2.481
   137 L      0.996**       9.869 +- 1.049



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:   0.446  0.258  0.141  0.074  0.039  0.020  0.011  0.006  0.003  0.002
w2:   0.000  0.000  0.000  0.000  0.002  0.009  0.032  0.098  0.257  0.602

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.001 0.000 0.000
 0.000 0.001 0.001 0.000 0.000
 0.000 0.000 0.001 0.002 0.003 0.000 0.000
 0.000 0.000 0.000 0.001 0.002 0.005 0.006 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.002 0.006 0.010 0.011 0.001 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.014 0.022 0.021 0.001 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.013 0.034 0.044 0.037 0.001 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.032 0.078 0.083 0.059 0.002 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.018 0.076 0.162 0.142 0.084 0.002 0.000

sum of density on p0-p1 =   1.000000
