
seed used = 140024133

K12                                  GTG GCG ATT AAT TTC AGC CCT AAG GTT GGT GAA ATA CTG GAA TGC AAC TTT GGT AAC TAT CCT GTT AGC CAA AAT GGA CCG TTC AGC ACG ACG TAT TAC GAT GGC CGC ATT CCT CCT GAA ATG ATA AAA AAC AGG TTA GTT GTC GTG CTC AAC GGA AAA ATT AAT GGC AAC GCA TGC ATC GTC GTT CCA TTA TCA ACC ACT CGC GAC CAG ACA AGT 
O157                                 GTG GCG ATT AAT TTC AGC CCT AAG GTT GGT GAA ATA CTG GAA TGC AAC TTT GGT AAC TAT CCT GTT AGC CAA AAT GGA CCG TTC AGC ACG ACG TAT TAC GAT GGC CGC ATT CCT CCT GAA ATG ATA AAA AAC AGG TTA GTT GTC GTG CTC AAC GGA AAA ATT AAT GGC AAC GCA TTC ATC GTC GTT CCA TTA TCA ACC ACT CGC GAC CAT GAC AAG 
EDL933                               GTG GCG ATT AAT TTC AGC CCT AAG GTT GGT GAA ATA CTG GAA TGC AAC TTT GGT AAC TAT CCT GTT AGC CAA AAT GGA CCG TTC AGC ACG ACG TAT TAC GAT GGC CGC ATT CCT CCT GAA ATG ATA AAA AAC AGG TTA GTT GTC GTG CTC AAC GGA AAA ATT AAT GGC AAC GCA TTC ATC GTC GTT CCA TTA TCA ACC ACT CGC GAC CAT GAC AAG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3777.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 72
# site patterns = 42
    2    1    3    3    2    3    4    1    4    2    3    2    1    1    5
    1    2    1    2    1    2    1    1    2    2    1    2    1    2    2
    1    1    1    1    1    1    1    1    1    1    1    1

1       
K12                   GTG GCG ATT AAT TTC AGC CCT AAG GTT GGT GAA ATA CTG TGC AAC TTT TAT CAA GGA CCG ACG TAC GAT GGC CGC ATG AAA AGG TTA GTC CTC GCA TGC ATC CCA TCA ACC ACT GAC CAG ACA AGT 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ..T GAC .AG 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ..T GAC .AG 

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

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

#1: K12            
position  1:    T:0.15278    C:0.16667    A:0.38889    G:0.29167
position  2:    T:0.30556    C:0.19444    A:0.29167    G:0.20833
position  3:    T:0.30556    C:0.31944    A:0.22222    G:0.15278

#2: O157           
position  1:    T:0.15278    C:0.16667    A:0.37500    G:0.30556
position  2:    T:0.31944    C:0.18056    A:0.31944    G:0.18056
position  3:    T:0.30556    C:0.33333    A:0.20833    G:0.15278

#3: EDL933         
position  1:    T:0.15278    C:0.16667    A:0.37500    G:0.30556
position  2:    T:0.31944    C:0.18056    A:0.31944    G:0.18056
position  3:    T:0.30556    C:0.33333    A:0.20833    G:0.15278

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


Codon position x base (3x4) table, overall

position  1:    T:0.15278    C:0.16667    A:0.37963    G:0.30093
position  2:    T:0.31481    C:0.18519    A:0.31019    G:0.18981
position  3:    T:0.30556    C:0.32870    A:0.21296    G:0.15278

Codon frequencies under model, for use in evolver:
  0.01505001  0.01619017  0.01048940  0.00752501
  0.00885295  0.00952363  0.00617024  0.00442647
  0.01482869  0.01595207  0.00000000  0.00000000
  0.00907427  0.00976172  0.00000000  0.00453714
  0.01641820  0.01766200  0.01144298  0.00820910
  0.00965776  0.01038941  0.00673117  0.00482888
  0.01617675  0.01740226  0.01127471  0.00808838
  0.00989921  0.01064915  0.00689945  0.00494960
  0.03739700  0.04023011  0.02606458  0.01869850
  0.02199824  0.02366477  0.01533210  0.01099912
  0.03684705  0.03963849  0.02568127  0.01842352
  0.02254819  0.02425639  0.01571541  0.01127410
  0.02964396  0.03188972  0.02066094  0.01482198
  0.01743763  0.01875866  0.01215350  0.00871881
  0.02920802  0.03142075  0.02035711  0.01460401
  0.01787357  0.01922762  0.01245733  0.00893678



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                 3.9744 (0.0402 0.0101)
EDL933               3.9744 (0.0402 0.0101)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 4
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -317.666796     +0.000000
   4..1     4..5     5..2     5..3  
  0.00000  0.15518  0.00000  0.00000  1.08788  0.93023  0.00000  0.00000 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.15520

(1: 0.000004, (2: 0.000004, 3: 0.000004): 0.155184);

(K12: 0.000004, (O157: 0.000004, EDL933: 0.000004): 0.155184);

Detailed output identifying parameters

kappa (ts/tv) =  1.08788


dN/dS for site classes (K=3)

p:   0.93023  0.00000  0.06977
w:   0.00000  1.00000999.00000

dN & dS for each branch

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

   4..1       0.000     49.1    166.9  69.6991   0.0000   0.0000    0.0    0.0
   4..5       0.155     49.1    166.9  69.6991   0.0667   0.0010    0.0   11.1
   5..2       0.000     49.1    166.9  69.6991   0.0000   0.0000    0.0    0.0
   5..3       0.000     49.1    166.9  69.6991   0.0000   0.0000    0.0    0.0


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

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

    59 C      1.000**       999.000
    70 Q      1.000**       999.000
    71 T      1.000**       999.000
    72 S      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 V      0.660         6.559 +- 4.283
     2 A      0.660         6.562 +- 4.282
     3 I      0.657         6.535 +- 4.290
     4 N      0.656         6.528 +- 4.292
     5 F      0.658         6.540 +- 4.288
     6 S      0.657         6.532 +- 4.291
     7 P      0.659         6.553 +- 4.285
     8 K      0.658         6.541 +- 4.288
     9 V      0.658         6.542 +- 4.288
    10 G      0.658         6.546 +- 4.287
    11 E      0.658         6.540 +- 4.289
    12 I      0.658         6.546 +- 4.287
    13 L      0.660         6.564 +- 4.281
    14 E      0.658         6.540 +- 4.289
    15 C      0.659         6.551 +- 4.285
    16 N      0.656         6.526 +- 4.293
    17 F      0.658         6.542 +- 4.288
    18 G      0.658         6.546 +- 4.287
    19 N      0.656         6.526 +- 4.293
    20 Y      0.658         6.547 +- 4.286
    21 P      0.659         6.553 +- 4.285
    22 V      0.658         6.542 +- 4.288
    23 S      0.657         6.532 +- 4.291
    24 Q      0.659         6.550 +- 4.285
    25 N      0.656         6.528 +- 4.292
    26 G      0.659         6.557 +- 4.283
    27 P      0.660         6.565 +- 4.281
    28 F      0.658         6.540 +- 4.288
    29 S      0.657         6.532 +- 4.291
    30 T      0.660         6.560 +- 4.283
    31 T      0.660         6.560 +- 4.283
    32 Y      0.658         6.547 +- 4.286
    33 Y      0.658         6.545 +- 4.287
    34 D      0.657         6.533 +- 4.290
    35 G      0.658         6.544 +- 4.287
    36 R      0.659         6.551 +- 4.285
    37 I      0.657         6.535 +- 4.290
    38 P      0.659         6.553 +- 4.285
    39 P      0.659         6.553 +- 4.285
    40 E      0.658         6.540 +- 4.289
    41 M      0.657         6.531 +- 4.291
    42 I      0.658         6.546 +- 4.287
    43 K      0.657         6.534 +- 4.290
    44 N      0.656         6.526 +- 4.293
    45 R      0.659         6.549 +- 4.286
    46 L      0.659         6.555 +- 4.284
    47 V      0.658         6.542 +- 4.288
    48 V      0.657         6.539 +- 4.289
    49 V      0.660         6.559 +- 4.283
    50 L      0.658         6.544 +- 4.287
    51 N      0.656         6.526 +- 4.293
    52 G      0.659         6.557 +- 4.283
    53 K      0.657         6.534 +- 4.290
    54 I      0.657         6.535 +- 4.290
    55 N      0.656         6.528 +- 4.292
    56 G      0.658         6.544 +- 4.287
    57 N      0.656         6.526 +- 4.293
    58 A      0.659         6.555 +- 4.284
    59 C      0.950*        9.136 +- 2.207
    60 I      0.657         6.532 +- 4.291
    61 V      0.657         6.539 +- 4.289
    62 V      0.658         6.542 +- 4.288
    63 P      0.660         6.561 +- 4.282
    64 L      0.659         6.555 +- 4.284
    65 S      0.660         6.565 +- 4.281
    66 T      0.657         6.539 +- 4.289
    67 T      0.658         6.542 +- 4.288
    68 R      0.659         6.551 +- 4.285
    69 D      0.656         6.530 +- 4.291
    70 Q      0.950*        9.136 +- 2.208
    71 T      0.999**       9.550 +- 1.218
    72 S      0.995**       9.514 +- 1.340



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:   0.098  0.098  0.099  0.099  0.100  0.100  0.101  0.101  0.102  0.102
w2:   0.000  0.000  0.001  0.003  0.010  0.028  0.067  0.141  0.270  0.480

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.001 0.001 0.000 0.000 0.000
 0.004 0.002 0.001 0.000 0.000 0.000 0.000
 0.009 0.005 0.004 0.002 0.001 0.000 0.000 0.000 0.000
 0.016 0.011 0.009 0.005 0.004 0.002 0.001 0.000 0.000 0.000 0.000
 0.027 0.019 0.016 0.011 0.008 0.005 0.004 0.002 0.001 0.000 0.000 0.000 0.000
 0.040 0.031 0.026 0.019 0.016 0.011 0.008 0.005 0.004 0.002 0.001 0.000 0.000 0.000 0.000
 0.057 0.045 0.040 0.030 0.026 0.019 0.016 0.010 0.008 0.005 0.004 0.002 0.001 0.000 0.000 0.000 0.000
 0.077 0.063 0.056 0.045 0.040 0.030 0.026 0.019 0.015 0.010 0.008 0.005 0.003 0.002 0.001 0.000 0.000 0.000 0.000

sum of density on p0-p1 =   1.000000
