
seed used = 140022905

K12                                  ATG ACT ACT TCC ATG CTC AAC GCA AAA CTA CTA CCA ACT GCG CCA TCC GCC GCA GTG GTC GTC GTG CGT GTG GTG GTG GTC GTC GGC AAT GCG CCG 
S2457T                               ATG ACT ACT TCC ATG TTC AAC GCA AAA CTA CTA CCA ACT GCG CCA TCC GCC GCA GTG GTC GTC GTG CGT GTG GTG GTG GTC GTC GGC AAT GCG CCG 
CFT073                               ATG ACT ACT TCC ATG TTC AAC GCA AAA CTA CTA CCA ACT GCG CCA TCC GCC GCA GTG GTC GTC GTG CGT GTG GTG GTG GTC GTC GGC AAT GCG CCG 
O157                                 ATG GCT ACT TCC ATG CTC AAC GCA AAA CTA CTA CCA ACT GCG CCA TCC GCC GCA GTG GTC GTC GTG CGT GTG GTG GTG GTC GTC GGC AAT GCG CCG 
EDL933                               ATG GCT ACT TCC ATG CTC AAC GCA AAA CTA CTA CCA ACT GCG CCA TCC GCC GCA GTG GTC GTC GTG CGT GTG GTG GTG GTC GTC GGC AAT GCG CCG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3672.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 32
# site patterns = 18
    2    1    2    2    1    1    2    1    2    2    2    1    5    4    1
    1    1    1

1       
K12                   ATG ACT ACT TCC CTC AAC GCA AAA CTA CCA GCG GCC GTG GTC CGT GGC AAT CCG 
S2457T                ... ... ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... 
O157                  ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
EDL933                ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.06250    C:0.21875    A:0.25000    G:0.46875
position  2:    T:0.43750    C:0.40625    A:0.09375    G:0.06250
position  3:    T:0.15625    C:0.31250    A:0.21875    G:0.31250

#2: S2457T         
position  1:    T:0.09375    C:0.18750    A:0.25000    G:0.46875
position  2:    T:0.43750    C:0.40625    A:0.09375    G:0.06250
position  3:    T:0.15625    C:0.31250    A:0.21875    G:0.31250

#3: CFT073         
position  1:    T:0.09375    C:0.18750    A:0.25000    G:0.46875
position  2:    T:0.43750    C:0.40625    A:0.09375    G:0.06250
position  3:    T:0.15625    C:0.31250    A:0.21875    G:0.31250

#4: O157           
position  1:    T:0.06250    C:0.21875    A:0.21875    G:0.50000
position  2:    T:0.43750    C:0.40625    A:0.09375    G:0.06250
position  3:    T:0.15625    C:0.31250    A:0.21875    G:0.31250

#5: EDL933         
position  1:    T:0.06250    C:0.21875    A:0.21875    G:0.50000
position  2:    T:0.43750    C:0.40625    A:0.09375    G:0.06250
position  3:    T:0.15625    C:0.31250    A:0.21875    G:0.31250

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       0 | Ser S TCT       0 | Tyr Y TAT       0 | Cys C TGT       0
      TTC       2 |       TCC      10 |       TAC       0 |       TGC       0
Leu L TTA       0 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       0 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       0 | His H CAT       0 | Arg R CGT       5
      CTC       3 |       CCC       0 |       CAC       0 |       CGC       0
      CTA      10 |       CCA      10 | Gln Q CAA       0 |       CGA       0
      CTG       0 |       CCG       5 |       CAG       0 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       0 | Thr T ACT      13 | Asn N AAT       5 | Ser S AGT       0
      ATC       0 |       ACC       0 |       AAC       5 |       AGC       0
      ATA       0 |       ACA       0 | Lys K AAA       5 | Arg R AGA       0
Met M ATG      10 |       ACG       0 |       AAG       0 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       0 | Ala A GCT       2 | Asp D GAT       0 | Gly G GGT       0
      GTC      20 |       GCC       5 |       GAC       0 |       GGC       5
      GTA       0 |       GCA      10 | Glu E GAA       0 |       GGA       0
      GTG      25 |       GCG      10 |       GAG       0 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.07500    C:0.20625    A:0.23750    G:0.48125
position  2:    T:0.43750    C:0.40625    A:0.09375    G:0.06250
position  3:    T:0.15625    C:0.31250    A:0.21875    G:0.31250

Codon frequencies under model, for use in evolver:
  0.00515148  0.01030296  0.00721207  0.01030296
  0.00478352  0.00956703  0.00669692  0.00956703
  0.00110389  0.00220778  0.00000000  0.00000000
  0.00073593  0.00147185  0.00000000  0.00147185
  0.01416656  0.02833313  0.01983319  0.02833313
  0.01315467  0.02630933  0.01841653  0.02630933
  0.00303569  0.00607138  0.00424997  0.00607138
  0.00202379  0.00404759  0.00283331  0.00404759
  0.01631301  0.03262603  0.02283822  0.03262603
  0.01514780  0.03029560  0.02120692  0.03029560
  0.00349565  0.00699129  0.00489390  0.00699129
  0.00233043  0.00466086  0.00326260  0.00466086
  0.03305532  0.06611063  0.04627744  0.06611063
  0.03069422  0.06138845  0.04297191  0.06138845
  0.00708328  0.01416656  0.00991660  0.01416656
  0.00472219  0.00944438  0.00661106  0.00944438



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                 
S2457T              -1.0000 (0.0149 0.0000)
CFT073              -1.0000 (0.0149 0.0000)-1.0000 (0.0000 0.0000)
O157                -1.0000 (0.0150 0.0000)-1.0000 (0.0302 0.0000)-1.0000 (0.0302 0.0000)
EDL933              -1.0000 (0.0150 0.0000)-1.0000 (0.0302 0.0000)-1.0000 (0.0302 0.0000)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, (4, 5)));   MP score: 3
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):   -129.850549     +0.000000
   6..7     7..1     7..2     6..8     8..3     8..9     9..4     9..5  
  0.00000  0.05640  0.00000  0.00000  0.00000  0.17817  0.00000  0.00000 99.00000  0.91313  0.00000  0.00000 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.23459

((1: 0.056396, 2: 0.000004): 0.000000, (3: 0.000004, (4: 0.000004, 5: 0.000004): 0.178174): 0.000000);

((K12: 0.056396, S2457T: 0.000004): 0.000000, (CFT073: 0.000004, (O157: 0.000004, EDL933: 0.000004): 0.178174): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) = 99.00000


dN/dS for site classes (K=3)

p:   0.91313  0.00000  0.08687
w:   0.00000  1.00000999.00000

dN & dS for each branch

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

   6..7       0.000     31.3     64.7  86.7856   0.0000   0.0000    0.0    0.0
   7..1       0.056     31.3     64.7  86.7856   0.0278   0.0003    0.0    1.8
   7..2       0.000     31.3     64.7  86.7856   0.0000   0.0000    0.0    0.0
   6..8       0.000     31.3     64.7  86.7856   0.0000   0.0000    0.0    0.0
   8..3       0.000     31.3     64.7  86.7856   0.0000   0.0000    0.0    0.0
   8..9       0.178     31.3     64.7  86.7856   0.0877   0.0010    0.0    5.7
   9..4       0.000     31.3     64.7  86.7856   0.0000   0.0000    0.0    0.0
   9..5       0.000     31.3     64.7  86.7856   0.0000   0.0000    0.0    0.0


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

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

     2 T      1.000**       999.000
     6 L      1.000**       999.000


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

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

     1 M      0.540         4.957 +- 4.127
     2 T      0.899         7.808 +- 2.930
     3 T      0.546         4.999 +- 4.127
     4 S      0.546         5.004 +- 4.127
     5 M      0.540         4.957 +- 4.127
     6 L      0.983*        8.423 +- 2.133
     7 N      0.548         5.015 +- 4.127
     8 A      0.544         4.987 +- 4.127
     9 K      0.548         5.018 +- 4.127
    10 L      0.548         5.015 +- 4.127
    11 L      0.548         5.015 +- 4.127
    12 P      0.547         5.010 +- 4.127
    13 T      0.546         4.999 +- 4.127
    14 A      0.542         4.970 +- 4.127
    15 P      0.547         5.010 +- 4.127
    16 S      0.546         5.004 +- 4.127
    17 A      0.542         4.970 +- 4.127
    18 A      0.544         4.987 +- 4.127
    19 V      0.542         4.972 +- 4.127
    20 V      0.542         4.972 +- 4.127
    21 V      0.542         4.972 +- 4.127
    22 V      0.542         4.972 +- 4.127
    23 R      0.549         5.024 +- 4.127
    24 V      0.542         4.972 +- 4.127
    25 V      0.542         4.972 +- 4.127
    26 V      0.542         4.972 +- 4.127
    27 V      0.542         4.972 +- 4.127
    28 V      0.542         4.972 +- 4.127
    29 G      0.547         5.014 +- 4.127
    30 N      0.548         5.020 +- 4.127
    31 A      0.542         4.970 +- 4.127
    32 P      0.546         5.004 +- 4.127



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:   0.097  0.098  0.098  0.099  0.100  0.100  0.101  0.101  0.102  0.103
w2:   0.003  0.008  0.018  0.034  0.057  0.086  0.123  0.168  0.221  0.281

Posterior for p0-p1 (see the ternary graph)

 0.001
 0.003 0.001 0.001
 0.005 0.003 0.002 0.001 0.001
 0.009 0.006 0.005 0.003 0.002 0.001 0.000
 0.013 0.010 0.009 0.006 0.005 0.003 0.002 0.001 0.000
 0.018 0.014 0.013 0.010 0.009 0.006 0.005 0.003 0.002 0.001 0.000
 0.022 0.019 0.017 0.014 0.013 0.010 0.009 0.006 0.005 0.003 0.002 0.001 0.000
 0.027 0.024 0.022 0.019 0.017 0.014 0.013 0.010 0.008 0.006 0.005 0.003 0.002 0.001 0.000
 0.032 0.029 0.027 0.024 0.022 0.019 0.017 0.014 0.012 0.010 0.008 0.006 0.005 0.003 0.002 0.001 0.000
 0.037 0.034 0.032 0.029 0.027 0.024 0.022 0.019 0.017 0.014 0.012 0.009 0.008 0.006 0.005 0.003 0.002 0.001 0.000

sum of density on p0-p1 =   1.000000
