
seed used = 141369193

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b0913.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 2  	ls = 754
# site patterns = 105
   17   11    9   11    6    7    2    6    4   25    1   15   18   13   21
   29    8   32   14   15   22    9   14   20    8   12    6   12   19   17
   16   11   13   39   17    8    6    2   15   14   14    4    1    5   18
    3    6    1    6    1    1    1   15    1    9    1    1    1    1   10
    8    1   10    1    4    4    1    1    5    6   10    4    1    6    1
    1    2    6    1    3    1    1    1    9    1    1    1    1    2    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1


1       
K12                   ATG AAA ATA ACG ACA GTC GGT GTA TGC ATT AGC GGA TTT CCG TTG CTG CCC CAA CCT GGG TTA ACC CTT GCG ACT CTC TTC GCC GCA ATC GTT CGT TAT TGG GGC TCA AAG TGG GAA CAG GAT GAG GCA GAC CAT TAC GGT CAT CTA CGA TCA CTC GTG ATG TGT GCT CAA GCA GGC AAT AGC CGT AGT GTC CGG TCC CCC CGC TCG CAC GCT CGC ATA CCA TTG ATG GGA CGA GCC TCT ATA GAG CCG AAC TGT GGA CAG CTG AGA ACA ATT AGC GAT ATA AGC TCG CTG CAA ATT CCA CAA GGT ACA AAT AGG 
O157                  ... ... ... ... ... ... ..C ... ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ..T ... ... ... ... T.. ... .A. C.. ..T ... C.. ... ..C .TG ..C ..T ... ... ..C ... ..T ... ... ..T ..T ... ... ... ... ..G ... C.. G.T ..T ... .T. ... ..T ..T ..A ... C.. .T. ..A G.. ... ..G ..C ..T ..C .C. C.. ..A .AA ACG C.. ..T ..G ..G GT. G.. ... 

Codon usage in sequences
--------------------------------------------------------------
Phe TTT 18 18 | Ser TCT  3  3 | Tyr TAT 13 14 | Cys TGT 10  9
    TTC  6  6 |     TCC  4  4 |     TAC  3  3 |     TGC  4  5
Leu TTA 22 22 |     TCA  9  9 | *** TAA  0  0 | *** TGA  0  0
    TTG 22 23 |     TCG  6  5 |     TAG  0  0 | Trp TGG 41 39
--------------------------------------------------------------
Leu CTT 14 16 | Pro CCT 14 16 | His CAT 19 18 | Arg CGT 12 13
    CTC 13 12 |     CCC  9  8 |     CAC  6  6 |     CGC  5  6
    CTA  6  6 |     CCA  7  8 | Gln CAA 35 35 |     CGA  7  6
    CTG 31 32 |     CCG 14 13 |     CAG 15 15 |     CGG  4  4
--------------------------------------------------------------
Ile ATT 27 26 | Thr ACT  8  8 | Asn AAT 11 10 | Ser AGT 10 11
    ATC 17 18 |     ACC  9  9 |     AAC  9  9 |     AGC 11  8
    ATA 12  9 |     ACA  8  7 | Lys AAA 11 11 | Arg AGA  2  2
Met ATG 19 18 |     ACG 11 13 |     AAG  6  6 |     AGG  1  1
--------------------------------------------------------------
Val GTT 16 18 | Ala GCT 11 11 | Asp GAT 15 16 | Gly GGT  9  9
    GTC  8  8 |     GCC 13 14 |     GAC  5  6 |     GGC 18 19
    GTA  6  8 |     GCA 21 19 | Glu GAA 15 15 |     GGA 18 15
    GTG 15 16 |     GCG 20 20 |     GAG  5  4 |     GGG 15 16
--------------------------------------------------------------

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

#1: K12            
position  1:    T:0.21353    C:0.27984    A:0.22812    G:0.27851
position  2:    T:0.33422    C:0.22149    A:0.22281    G:0.22149
position  3:    T:0.27851    C:0.18568    A:0.23740    G:0.29841

#2: O157           
position  1:    T:0.21220    C:0.28382    A:0.22016    G:0.28382
position  2:    T:0.33952    C:0.22149    A:0.22281    G:0.21618
position  3:    T:0.28647    C:0.18700    A:0.22812    G:0.29841

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      36 | Ser S TCT       6 | Tyr Y TAT      27 | Cys C TGT      19
      TTC      12 |       TCC       8 |       TAC       6 |       TGC       9
Leu L TTA      44 |       TCA      18 | *** * TAA       0 | *** * TGA       0
      TTG      45 |       TCG      11 |       TAG       0 | Trp W TGG      80
------------------------------------------------------------------------------
Leu L CTT      30 | Pro P CCT      30 | His H CAT      37 | Arg R CGT      25
      CTC      25 |       CCC      17 |       CAC      12 |       CGC      11
      CTA      12 |       CCA      15 | Gln Q CAA      70 |       CGA      13
      CTG      63 |       CCG      27 |       CAG      30 |       CGG       8
------------------------------------------------------------------------------
Ile I ATT      53 | Thr T ACT      16 | Asn N AAT      21 | Ser S AGT      21
      ATC      35 |       ACC      18 |       AAC      18 |       AGC      19
      ATA      21 |       ACA      15 | Lys K AAA      22 | Arg R AGA       4
Met M ATG      37 |       ACG      24 |       AAG      12 |       AGG       2
------------------------------------------------------------------------------
Val V GTT      34 | Ala A GCT      22 | Asp D GAT      31 | Gly G GGT      18
      GTC      16 |       GCC      27 |       GAC      11 |       GGC      37
      GTA      14 |       GCA      40 | Glu E GAA      30 |       GGA      33
      GTG      31 |       GCG      40 |       GAG       9 |       GGG      31
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.21286    C:0.28183    A:0.22414    G:0.28117
position  2:    T:0.33687    C:0.22149    A:0.22281    G:0.21883
position  3:    T:0.28249    C:0.18634    A:0.23276    G:0.29841

Codon frequencies under model, for use in evolver:
  0.02101421  0.01386148  0.01731452  0.02219811
  0.01381643  0.00911365  0.01138396  0.01459482
  0.01389916  0.00916823  0.00000000  0.00000000
  0.01365096  0.00900451  0.00000000  0.01442003
  0.02782255  0.01835243  0.02292421  0.02939002
  0.01829278  0.01206636  0.01507222  0.01932336
  0.01840232  0.01213862  0.01516247  0.01943907
  0.01807370  0.01192186  0.01489171  0.01909194
  0.02212711  0.01459558  0.01823149  0.02337371
  0.01454814  0.00959631  0.01198685  0.01536775
  0.01463525  0.00965377  0.01205862  0.01545977
  0.01437391  0.00948138  0.01184329  0.01518371
  0.02775708  0.01830925  0.02287027  0.02932086
  0.01824974  0.01203797  0.01503675  0.01927789
  0.01835902  0.01211006  0.01512679  0.01939333
  0.01803118  0.01189380  0.01485667  0.01904702



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                 0.2715 (0.0145 0.0533)


TREE #  1:  (1, 2);   MP score: 47
lnL(ntime:  2  np:  7):  -3361.803668     +0.000000
   3..1     3..2  
  0.05563  0.15189  2.64422  0.99449  0.00000  0.28560 300.89889
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.20752

(1: 0.055629, 2: 0.151895);

(K12: 0.055629, O157: 0.151895);

Detailed output identifying parameters

kappa (ts/tv) =  2.64422


dN/dS for site classes (K=3)

p:   0.99449  0.00000  0.00551
w:   0.28560  1.00000300.89889

dN & dS for each branch

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

   3..1       0.056    684.1   1577.9   1.9407   0.0217   0.0112    7.7   34.3
   3..2       0.152    684.1   1577.9   1.9407   0.0593   0.0306   20.9   93.6


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

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

   128 Q      0.525         158.017
   285 M      0.589         177.488
   706 L      0.525         158.017
   710 Q      0.998**       300.406
   720 T      0.746         224.591


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

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

    12 S      0.507         3.773 +- 3.672
   128 Q      0.515         3.840 +- 3.689
   285 M      0.713         5.173 +- 3.591
   482 G      0.501         3.733 +- 3.664
   612 S      0.507         3.774 +- 3.672
   706 L      0.515         3.840 +- 3.689
   710 Q      0.890         6.249 +- 3.072
   720 T      0.866         6.099 +- 3.158



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:   0.562  0.325  0.096  0.015  0.002  0.000  0.000  0.000  0.000  0.000
w2:   0.058  0.065  0.076  0.093  0.107  0.116  0.122  0.124  0.123  0.117

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 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.022
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.012 0.108
 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 0.003 0.010 0.048 0.276
 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 0.002 0.005 0.010 0.026 0.141 0.327

sum of density on p0-p1 =   1.000000
