
seed used = 139999729

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1507.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 188
# site patterns = 66
    7    1    5    3    5    3    3    1    4    1    7    8    4    5    7
    2    7    2    6    3    2    2    8    5    2    1    3    2    1    1
    1    2    1    5   10    5    1    1    3    4    2    1    2    3    2
    2    2    4    2    1    1    4    3    2    1    1    1    1    1    1
    1    1    1    1    2    1

K12                                  ATG TGT CAG ACA TTC GGT TTA CCT TCA TCG GTG AAA TAT GAA GAT GGA GGC CCA ATC GCG CGG GCT TTT TTG GGG TCC AGC GAG CTG AAA CGC GTC TGG ATT GCA ACG GAC GGT CAT AAC TCC GTA AGT CGA CTC TAC GAC CCG CTT ATA CAC CTG AAG AGA GCC CCA ACT CCG GTT AGC AAT AGG CAT GGA --- AGT 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ..T CGC ..T ... ... ... ... ... ..T ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ..A ... .C. ... ... ..C ..T --- .T. 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ..T CGC ..T ... ... ... ... ... ..T ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ..A ... .C. ... ... ..C ..T --- .T. 



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT  8  8  8 | Ser TCT  0  0  0 | Tyr TAT  4  4  4 | Cys TGT  1  1  1
    TTC  5  6  6 |     TCC  3  2  2 |     TAC  2  2  2 |     TGC  0  0  0
Leu TTA  3  3  3 |     TCA  4  4  4 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  5  5  5 |     TCG  1  1  1 |     TAG  0  0  0 | Trp TGG  1  1  1
--------------------------------------------------------------------------
Leu CTT  2  3  3 | Pro CCT  1  1  1 | His CAT  4  3  3 | Arg CGT  0  1  1
    CTC  2  2  2 |     CCC  0  0  0 |     CAC  1  2  2 |     CGC  1  1  1
    CTA  0  0  0 |     CCA  3  3  3 | Gln CAA  0  0  0 |     CGA  3  3  3
    CTG  5  4  4 |     CCG  5  5  5 |     CAG  5  5  5 |     CGG  2  2  2
--------------------------------------------------------------------------
Ile ATT  5  6  6 | Thr ACT  1  1  1 | Asn AAT  1  1  1 | Ser AGT  3  2  2
    ATC  6  6  6 |     ACC  0  1  1 |     AAC  4  4  4 |     AGC  4  3  3
    ATA  1  1  1 |     ACA  3  3  3 | Lys AAA  9  8  8 | Arg AGA  2  2  2
Met ATG  7  7  7 |     ACG  5  5  5 |     AAG  3  3  3 |     AGG  1  1  1
--------------------------------------------------------------------------
Val GTT  1  1  1 | Ala GCT  2  2  2 | Asp GAT  7  8  8 | Gly GGT  4  4  4
    GTC  2  2  2 |     GCC  1  1  1 |     GAC  3  2  2 |     GGC  7  8  8
    GTA  1  1  1 |     GCA 10 10 10 | Glu GAA  5  5  5 |     GGA  3  2  2
    GTG  7  7  7 |     GCG  3  3  3 |     GAG  2  2  2 |     GGG  2  2  2
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.19892    C:0.18280    A:0.29570    G:0.32258
position  2:    T:0.32258    C:0.22581    A:0.26882    G:0.18280
position  3:    T:0.23656    C:0.22043    A:0.25269    G:0.29032

#2: O157           
position  1:    T:0.19892    C:0.18817    A:0.29032    G:0.32258
position  2:    T:0.33333    C:0.22581    A:0.26344    G:0.17742
position  3:    T:0.24731    C:0.22581    A:0.24194    G:0.28495

#3: EDL933         
position  1:    T:0.19892    C:0.18817    A:0.29032    G:0.32258
position  2:    T:0.33333    C:0.22581    A:0.26344    G:0.17742
position  3:    T:0.24731    C:0.22581    A:0.24194    G:0.28495

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      24 | Ser S TCT       0 | Tyr Y TAT      12 | Cys C TGT       3
      TTC      17 |       TCC       7 |       TAC       6 |       TGC       0
Leu L TTA       9 |       TCA      12 | *** * TAA       0 | *** * TGA       0
      TTG      15 |       TCG       3 |       TAG       0 | Trp W TGG       3
------------------------------------------------------------------------------
Leu L CTT       8 | Pro P CCT       3 | His H CAT      10 | Arg R CGT       2
      CTC       6 |       CCC       0 |       CAC       5 |       CGC       3
      CTA       0 |       CCA       9 | Gln Q CAA       0 |       CGA       9
      CTG      13 |       CCG      15 |       CAG      15 |       CGG       6
------------------------------------------------------------------------------
Ile I ATT      17 | Thr T ACT       3 | Asn N AAT       3 | Ser S AGT       7
      ATC      18 |       ACC       2 |       AAC      12 |       AGC      10
      ATA       3 |       ACA       9 | Lys K AAA      25 | Arg R AGA       6
Met M ATG      21 |       ACG      15 |       AAG       9 |       AGG       3
------------------------------------------------------------------------------
Val V GTT       3 | Ala A GCT       6 | Asp D GAT      23 | Gly G GGT      12
      GTC       6 |       GCC       3 |       GAC       7 |       GGC      23
      GTA       3 |       GCA      30 | Glu E GAA      15 |       GGA       7
      GTG      21 |       GCG       9 |       GAG       6 |       GGG       6
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.19892    C:0.18638    A:0.29211    G:0.32258
position  2:    T:0.32975    C:0.22581    A:0.26523    G:0.17921
position  3:    T:0.24373    C:0.22401    A:0.24552    G:0.28674

Codon frequencies under model, for use in evolver:
  0.01659880  0.01525625  0.01672085  0.01952800
  0.01136657  0.01044721  0.01145014  0.01337243
  0.01335121  0.01227133  0.00000000  0.00000000
  0.00902108  0.00829144  0.00000000  0.01061304
  0.01555202  0.01429414  0.01566638  0.01829650
  0.01064976  0.00978838  0.01072806  0.01252912
  0.01250924  0.01149746  0.01260122  0.01471675
  0.00845219  0.00776855  0.00851434  0.00994375
  0.02437481  0.02240332  0.02455403  0.02867624
  0.01669144  0.01534140  0.01681418  0.01963699
  0.01960582  0.01802006  0.01974998  0.02306568
  0.01324718  0.01217572  0.01334458  0.01558492
  0.02691697  0.02473986  0.02711489  0.03166702
  0.01843227  0.01694142  0.01856780  0.02168502
  0.02165060  0.01989945  0.02180980  0.02547130
  0.01462879  0.01344558  0.01473635  0.01721034



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                 0.1932 (0.0130 0.0674)
EDL933               0.1932 (0.0130 0.0674)-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):   -828.080483     +0.000000
   4..1     4..5     5..2     5..3  
  0.32706  0.00000  0.00000  0.00000  2.26148  0.99332  0.00000  0.12473 324.04437
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.32707

(1: 0.327062, (2: 0.000004, 3: 0.000004): 0.000000);

(K12: 0.327062, (O157: 0.000004, EDL933: 0.000004): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.26148


dN/dS for site classes (K=3)

p:   0.99332  0.00000  0.00668
w:   0.12473  1.00000324.04437

dN & dS for each branch

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

   4..1       0.327    157.5    406.5   2.2880   0.1294   0.0565    8.9   52.6
   4..5       0.000    157.5    406.5   2.2880   0.0000   0.0000    0.0    0.0
   5..2       0.000    157.5    406.5   2.2880   0.0000   0.0000    0.0    0.0
   5..3       0.000    157.5    406.5   2.2880   0.0000   0.0000    0.0    0.0


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

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

    36 K      1.000**       323.898


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

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

    36 K      0.960*        6.989 +- 2.753
   170 S      0.515         4.034 +- 3.848



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:   0.685  0.232  0.063  0.015  0.003  0.001  0.000  0.000  0.000  0.000
w2:   0.038  0.048  0.064  0.081  0.098  0.113  0.126  0.136  0.145  0.151

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.015
 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 0.008 0.061
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.030 0.205
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.004 0.014 0.106 0.540

sum of density on p0-p1 =   1.000000
