
seed used = 140030901

K12                                  GTG TTG CTG AAG TTA CTG ATT ATC TTG GTA TTA ACC CCC CGA GCC TCT ACG CGG CTT TTG GCA GTA AAG CTG GGT TAT TTA GCC GTG TAC TCA ATG AAT ACG TCG GTA CGG AAG CTA TTC CGC TTG CCG ATA TTC TTC GTG ATG ATC GTC CGG 
S2457T                               GTG TCT CTG AAG TTA CTG ATT ATC TTG GTA TTA ACC CCC CGA GTC TCT ACG CGG CTT TTG GCA GTA AGG CTG GGT TAT TTA GCC GTG TAC TCA ATG AAT ATG TCG GTA CGG AAG CTA TTC CGC TTG CCG ATA TTC TTC GTG ATG ATC GTC CGG 
O157                                 GTG TTG CTG AAG TTA CTG ATT ATC TTG GTA TTA ACC CCC CGA GCC TCT ACG CGG CTT TTG GCA GTA AGG CTG GGT TAT TTA GCC GTG TAC TCA ATG AAT ATG TCG GTA CGG AAG CTA TTC CGC TTG TCG ATA TTC TTC GTG ATG ATC GTC CGG 
EDL933                               GTG TTG CTG AAG TTA CTG ATT ATC TTG GTA TTA ACC CCC CGA GCC TCT ACG CGG CTT TTG GCA GTA AGG CTG GGT TAT TTA GCC GTG TAC TCA ATG AAT ATG TCG GTA CGG AAG CTA TTC CGC TTG TCG ATA TTC TTC GTG ATG ATC GTC CGG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4250.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 51
# site patterns = 34
    3    1    3    2    3    1    2    3    3    1    1    1    1    1    1
    3    1    1    1    1    1    1    1    1    2    1    1    1    1    3
    1    1    1    1

1       
K12                   GTG TTG CTG AAG TTA ATT ATC TTG GTA ACC CCC CGA GCC TCT ACG CGG CTT GCA AAG GGT TAT GCC TAC TCA ATG AAT ACG TCG CTA TTC CGC CCG ATA GTC 
S2457T                ... .CT ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... .G. ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... .T. ... ... ... ... T.. ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... .T. ... ... ... ... T.. ... ... 

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

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

#1: K12            
position  1:    T:0.29412    C:0.23529    A:0.25490    G:0.21569
position  2:    T:0.54902    C:0.21569    A:0.11765    G:0.11765
position  3:    T:0.11765    C:0.23529    A:0.21569    G:0.43137

#2: S2457T         
position  1:    T:0.29412    C:0.23529    A:0.25490    G:0.21569
position  2:    T:0.56863    C:0.19608    A:0.09804    G:0.13725
position  3:    T:0.13725    C:0.23529    A:0.21569    G:0.41176

#3: O157           
position  1:    T:0.31373    C:0.21569    A:0.25490    G:0.21569
position  2:    T:0.56863    C:0.19608    A:0.09804    G:0.13725
position  3:    T:0.11765    C:0.23529    A:0.21569    G:0.43137

#4: EDL933         
position  1:    T:0.31373    C:0.21569    A:0.25490    G:0.21569
position  2:    T:0.56863    C:0.19608    A:0.09804    G:0.13725
position  3:    T:0.11765    C:0.23529    A:0.21569    G:0.43137

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


Codon position x base (3x4) table, overall

position  1:    T:0.30392    C:0.22549    A:0.25490    G:0.21569
position  2:    T:0.56373    C:0.20098    A:0.10294    G:0.13235
position  3:    T:0.12255    C:0.23529    A:0.21569    G:0.42647

Codon frequencies under model, for use in evolver:
  0.02161799  0.04150655  0.03804767  0.07523062
  0.00770728  0.01479799  0.01356482  0.02682135
  0.00394763  0.00757946  0.00000000  0.00000000
  0.00507553  0.00974502  0.00000000  0.01766284
  0.01603916  0.03079518  0.02822892  0.05581627
  0.00571831  0.01097915  0.01006422  0.01989971
  0.00292889  0.00562347  0.00515485  0.01019254
  0.00376572  0.00723017  0.00662766  0.01310469
  0.01813122  0.03481194  0.03191095  0.06309665
  0.00646417  0.01241121  0.01137695  0.02249533
  0.00331092  0.00635696  0.00582722  0.01152200
  0.00425690  0.00817324  0.00749214  0.01481400
  0.01534180  0.02945626  0.02700157  0.05338947
  0.00546969  0.01050180  0.00962665  0.01903451
  0.00280155  0.00537897  0.00493072  0.00974938
  0.00360199  0.00691582  0.00633950  0.01253492



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               3.6773 (0.0424 0.0115)
O157                -1.0000 (0.0280 0.0000) 2.8100 (0.0326 0.0116)
EDL933              -1.0000 (0.0280 0.0000) 2.8100 (0.0326 0.0116)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, 4));   MP score: 5
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):   -225.920606     +0.000000
   5..6     6..1     6..2     5..7     7..3     7..4  
  0.00000  0.04510  0.08219  0.02238  0.00000  0.00000 15.60139  0.72810  0.00000  1.00000 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.14967

((1: 0.045098, 2: 0.082191): 0.000000, (3: 0.000004, 4: 0.000004): 0.022377);

((K12: 0.045098, S2457T: 0.082191): 0.000000, (O157: 0.000004, EDL933: 0.000004): 0.022377);

Detailed output identifying parameters

kappa (ts/tv) = 15.60139


dN/dS for site classes (K=3)

p:   0.72810  0.00000  0.27190
w:   1.00000  1.00000999.00000

dN & dS for each branch

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

   5..6       0.000     60.6     92.4 272.3558   0.0000   0.0000    0.0    0.0
   6..1       0.045     60.6     92.4 272.3558   0.0248   0.0001    0.0    2.3
   6..2       0.082     60.6     92.4 272.3558   0.0453   0.0002    0.0    4.2
   5..7       0.022     60.6     92.4 272.3558   0.0123   0.0000    0.0    1.1
   7..3       0.000     60.6     92.4 272.3558   0.0000   0.0000    0.0    0.0
   7..4       0.000     60.6     92.4 272.3558   0.0000   0.0000    0.0    0.0


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

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

     2 L      1.000**       998.991
    15 A      0.996**       994.693
    23 K      0.996**       995.429
    34 T      0.993**       992.302
    43 P      0.995**       993.563


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

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

     1 V      0.722         7.072 +- 4.057
     2 L      0.992**       9.427 +- 1.465
     3 L      0.723         7.082 +- 4.053
     4 K      0.723         7.081 +- 4.053
     5 L      0.723         7.083 +- 4.052
     6 L      0.723         7.082 +- 4.053
     7 I      0.723         7.082 +- 4.053
     8 I      0.723         7.078 +- 4.054
     9 L      0.723         7.080 +- 4.054
    10 V      0.723         7.079 +- 4.054
    11 L      0.723         7.083 +- 4.052
    12 T      0.723         7.079 +- 4.054
    13 P      0.723         7.079 +- 4.054
    14 R      0.724         7.085 +- 4.051
    15 A      0.964*        9.188 +- 2.026
    16 S      0.723         7.082 +- 4.053
    17 T      0.722         7.073 +- 4.057
    18 R      0.723         7.081 +- 4.053
    19 L      0.723         7.081 +- 4.053
    20 L      0.723         7.080 +- 4.054
    21 A      0.723         7.080 +- 4.054
    22 V      0.723         7.079 +- 4.054
    23 K      0.964*        9.188 +- 2.025
    24 L      0.723         7.082 +- 4.053
    25 G      0.724         7.085 +- 4.051
    26 Y      0.724         7.084 +- 4.052
    27 L      0.723         7.083 +- 4.052
    28 A      0.723         7.079 +- 4.054
    29 V      0.722         7.072 +- 4.057
    30 Y      0.724         7.083 +- 4.052
    31 S      0.723         7.078 +- 4.054
    32 M      0.722         7.068 +- 4.059
    33 N      0.724         7.084 +- 4.052
    34 T      0.963*        9.186 +- 2.029
    35 S      0.722         7.071 +- 4.058
    36 V      0.723         7.079 +- 4.054
    37 R      0.723         7.081 +- 4.053
    38 K      0.723         7.081 +- 4.053
    39 L      0.724         7.084 +- 4.052
    40 F      0.723         7.077 +- 4.055
    41 R      0.724         7.083 +- 4.052
    42 L      0.723         7.080 +- 4.054
    43 P      0.963*        9.187 +- 2.027
    44 I      0.722         7.070 +- 4.058
    45 F      0.723         7.077 +- 4.055
    46 F      0.723         7.077 +- 4.055
    47 V      0.722         7.072 +- 4.057
    48 M      0.722         7.068 +- 4.059
    49 I      0.723         7.078 +- 4.054
    50 V      0.723         7.078 +- 4.054
    51 R      0.723         7.081 +- 4.053



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:   0.096  0.097  0.098  0.098  0.099  0.100  0.101  0.102  0.103  0.104
w2:   0.000  0.000  0.001  0.005  0.013  0.033  0.072  0.144  0.267  0.465

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.001 0.000 0.000 0.000 0.000
 0.002 0.001 0.000 0.000 0.000 0.000 0.000
 0.005 0.003 0.002 0.001 0.000 0.000 0.000 0.000 0.000
 0.012 0.007 0.005 0.002 0.002 0.001 0.000 0.000 0.000 0.000 0.000
 0.024 0.015 0.011 0.007 0.005 0.002 0.002 0.001 0.000 0.000 0.000 0.000 0.000
 0.045 0.030 0.024 0.015 0.011 0.006 0.004 0.002 0.001 0.001 0.000 0.000 0.000 0.000 0.000
 0.078 0.054 0.044 0.029 0.023 0.014 0.011 0.006 0.004 0.002 0.001 0.001 0.000 0.000 0.000 0.000 0.000
 0.128 0.092 0.076 0.053 0.043 0.028 0.022 0.014 0.010 0.006 0.004 0.002 0.001 0.001 0.000 0.000 0.000 0.000 0.000

sum of density on p0-p1 =   1.000000
