
seed used = 140020809

K12                                  ATG TCA ATT GAC TTT ACC CCA GGT ATA ATA AAT ACA TAT CAC GGC GAT ATT TAT AAC TGC ACA ACA AAT ACC GAT AAT GCT AAA ACG CCA GAC ACA CCG AAG TGG CCT TGC GAT AAT TGG GAA GAA CAA CAA CCC ATT AAT TCC ACA TTC TCT GGA GAA GGA TAT ATC TCT GAT CAA TAT GAT TTA GCG CAA CAC CAA CTT CAA CAA ATT AAT GCG TGC CAC ACG AAC ACT ACA TAT ACA AAT GCA GAC TAC TCA AAA GTT GTG GCT CAA CTT GTA AGT CTT ATT ACT AAC ATT GAA ACG ATA AGT TCG ACA CAA CTT ACG CAA CAG ACA CAA TCA ATA CTT AAT CAG ATT AAT AAC ATT AGA TAT GAA AAA AAC AAA AGT GCT GAA TGT CGA ATC ATT GTT ATC GCT AAT CCT AAA CCC GAC AAG GCA ATC ATA ACT AAA ATT AGC GTA GAA GAG GGA ATA CCC ATA ACA TTC AGT GTC CAA ACC ATG TTT TCA GAT ACT AAT TTT ATT GCT GAA CAA CGA GCT GAC TTA CCA ACT AAT ATA AAA GAT ATT CAA AGC CTG TAT CAA AAA ATG ACG AAG TTA TAT ATT GAG CAC AGT GAA AAT AAA AAC AGG ATG AAA GTC TTT GCC GGA ACC AAC TTT ATT GAT TTC AAT ATG ACA GGA CAG AAC CTG TCC GGG TTC GTT CTA ACC TTG TCA AGG TTT TAT TTC GAA GAT CTA CTT AAT ATA AAT TTC ACT GAC GCA AAT TTA GGG --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- AAG GTG CGA ATA AGC GGG GAA ATT CTT CTC GGC 
Shig4337                             ATG TCA ATT GAC TTT ACC CCA GGT ATA ATA AAT ACA TAT CAC GGC GAT ATT TAT AAC TGC ACA ACA AAT ACC GAT AAT GTT AAA ACG CCA GAC ACA CCG AAG TGG CCT TGT GAT AAT TGG GAA GAA CAA CAA CCC ATT AAT TCC ACA TTC TCT GGA GAA GGA TAC AAC CCT GAA CAA TTT GAT TTA GCG CAA CAA CAA CTC CAA CAA ATT AAT GCA TGC CAC ACG AAC ACC ACA TAT ACA AAT GCA GAC TAC TCA AAA GTT GTG GTT CAA CTT GTA AGT CTT ATT AAT AAC ATT GAA ACG ATA AGT TCG ACA CCA CTT ACG CAA CAG ACA CAA TCA ATA CTT AAT CAG ATT CAT AAC ATT AGA TAC GAA AAG GAT AAG GAT TCT GTA TGT CAA ATC ATT GTT GTC GTT AAT CCA GAA CCC AAC AAT CCA ATC ATA ACT AAA ATT CTC GTA GAA GAA GGA ATA CCC GAA AGA TTC AGT GTC CAA ACC GTT TCT TCC GAT AAT AAA AAT TTT GCT GGG CAA CGA GCT GAC TTA CCA ACT GAT ATA AGA GAC ATT CAA AGC TTG TAC TTA AAA ATG GCG AAG CTG TAT ATT GAG CAC AGT AAA AAT GAA AAT AGG ATG GAA GCC CTT GCT GGA TGC GAC TTT ATT GAT TTC AAC ATG ACA GGG CAA GAT ATG TCC AAG CTA GTC CTA ACC TTA TCA AAA TTT TAT TTT GAA GAT CTA CTT AAT ATA AAT TTC ACT GAC GCA AAT TTA TTT AAC ACT ATT TTT TCA CAC AAG GAA AAT CCC ATC CCC AAA CTA CAT AAA TAT GAA CAA CAT CTT GAC AAA CAA ATC AAT GGT TTG TTT TCT ACA TTG TTA ACT ATT AAT GAC AAC TCT TTA CGC GCG AAA GCG GAA ATT GCT TCG AGA ATA ATT GAT TTC 
O157                                 ATG TCA ATT GAC TTT ACC CCA GGT ATG ATA AAT ACA TAT CAC GGC GAT ATT TAT AAC CGC ACA ACA GAT ACC GAC AAT GTT AAA ACA CCA GAC ACA CCG ATG TGG CCT TGT GAT AAT CGG GAA GAA CAA CAA CCC ATT AAT TCC ACA TTC TCT GGA GAA GGA TAC AAC CCT GAA CAA TAT GAT TTA GCG CGG CAA CAC CTC CCA CAA ATT TAT GCG TGC CGC ACG AAC ACC AAA TAT ACA GAT GCA GAC TAC TCA AAA GTT GTG GCT CAA CTT GTA AGT CTT ATT ACT AAC ATT GAA TCG ATA AGT TCG ACA CCA CTT ACG CGG CAG GCA CAG GAA ATA CTT AAT CAA ATT AAT AAC ATT AGA TAC GAA AAG AAC AAA AGT GCT GAA TGT CGA ATC ATT GTT GTC GCT AAT CCT AAA CCC GAC AAG GCA ATC ATA ACT AAA ATT AGC GTA GAA GAG GGA ATA CCA GTA AGA TTC AGT GTC CAA ACC ATG TTT TCA GAT ACT AAT TTT ATT GCT GAA CAA CGA GCT GAC TTA CCG ACT AAT ATA AAA GAT ATT CAA AGC CTG TAT CAA AAA ATG ACG AAG TTA TAT ATT GAG CAC AGT GAA AAT AAA AAC AGG ATG AAA GTC TTT GCC GGA ACC AAC TTT ATT GAT TTC AAT ATG ACA GGA CAG AAC CTG TCC GGG TTC GTT CTA ACC TTG TCA AGG TTT TAT TTC GAA GAT CTA CTT AAT ATA AAT TTC ACT GAC GCA AAT TTA GGT GAC ACT ATT TTT TCA CAT AAA GAA CAC CCT ACT CCA AAA TTA TAT AAA GAC GAA CAA TAT CTT GAC AAA CAA ATC GAA GGT TTA TTT TCA ACA TTA TTA ACC ATT AAT GAC AAC TTT TTA CGA GCA AAA GCG GAA ATT GCT TCG ACA ATA ATT AAA TTT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3504.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 302
# site patterns = 180
    4    3   13    5    3    4    2    1    1    7   10    8    5    2    1
    6    4    1    2    1    1    4    1    1    1    1    1    1    1    7
    8    2    2    4    1    4    2    1    1    1    1    3    1    2    1
    1    1    1    1    1    1    1    2    1    1    2    1    2    1    2
    5    2    4    2    1    1    1    1    1    1    1    1    1    1    1
    2    1    1    1    1    1    1    2    1    1    3    1    1    1    3
    1    1    1    1    1    1    1    1    1    1    1    1    2    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    2    1    1
    1    1    1    1    2    2    1    1    1    2    1    1    1    1    3
    1    2    1    2    1    2    1    1    1    2    1    1    2    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1


K12                                  ATG TCA ATT GAC TTT ACC CCA GGT ATA ATA AAT ACA TAT CAC GGC GAT AAC TGC AAT GAT GCT AAA ACG CCG AAG TGG CCT TGC TGG GAA CAA CCC TCC TTC TCT GGA TAT ATC TCT GAT TAT TTA GCG CAA CAC CAA CTT CAA AAT GCG TGC CAC ACG ACT ACA GCA TAC GTT GTG GCT CTT GTA AGT ACT ACG TCG CAA CAG ACA CAA TCA CAG AAT AGA AAA AAC AAA AGT GCT GAA TGT CGA ATC ATC CCT AAA GAC AAG GCA ACT AGC GAG CCC ATA ACA GTC ATG TTT TCA AAT TTT ATT GCT GAA CGA CCA AAT AAA GAT AGC CTG TAT CAA ACG AAG TTA GAG GAA AAC AGG GTC TTT GCC ACC AAC AAT GGA CAG CTG GGG TTC GTT CTA TTG AGG TTC GGG --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- AAG GTG CGA ATA AGC GGG GAA ATT CTT CTC GGC 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ..C .A. C.. ..A .T. ... ... ... ..A ... ..C ... ... ..A ... ... ... ..C ... ... ... ... ... .T. ... ... ... .A. ... ... .C. ... ... ... ... ... C.. ... ..G G.T ..G GA. T.. .T. ... .A. ... G.. ..A G.. A.. ..T C.. ... CT. ..A ... GA. .G. ... G.T .C. ..C ..A AA. T.. ... .GG ... ... G.. .G. ..C ... T.. ..C TT. G.. ... C.G ... A.. ..T ... .C. C.. ..T TG. G.. ..C ..G ..A A.. AA. C.A ..C ... ..A .AA ..T TTT AAC ACT ATT TTT TCA CAC AAG GAA AAT CCC ATC CCC AAA CTA CAT TAT CAA CTT GAC ATC AAT GGT TTG TCT ACA TTA ACT AAT AAC TCT CGC GCG ..A .C. GA. ..T GCT TC. AG. ..A A.. GAT TT. 
O157                                 ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... C.. G.. ..C .T. ... ..A ... .T. ... ... ..T C.. ... ... ... ... ... ... ... ..C .A. C.. ..A ... ... ... .GG ..A ..C ..C .C. T.. ... ... .G. ... ..C .A. ... ... ... ... ... ... ... ... ... T.. ... .C. ... G.. ..G GA. ..A ... ... ..G ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ..A G.. .G. ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T GAC ACT ATT TTT TCA CAT AAA GAA CAC CCT ACT CCA AAA TTA TAT GAC CAA CTT GAC ATC GAA GGT TTA TCA ACA TTA ACC AAT AAC TTT CGA GCA ..A .C. GA. ..T GCT TC. AC. ..A A.. AAA TTT 



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

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

#1: K12            
position  1:    T:0.16538    C:0.17692    A:0.42692    G:0.23077
position  2:    T:0.27692    C:0.22308    A:0.38077    G:0.11923
position  3:    T:0.34231    C:0.19615    A:0.32692    G:0.13462

#2: Shig4337       
position  1:    T:0.18543    C:0.18874    A:0.38742    G:0.23841
position  2:    T:0.28477    C:0.21854    A:0.40397    G:0.09272
position  3:    T:0.34768    C:0.19868    A:0.33775    G:0.11589

#3: O157           
position  1:    T:0.18212    C:0.17881    A:0.39404    G:0.24503
position  2:    T:0.27815    C:0.22848    A:0.38411    G:0.10927
position  3:    T:0.33444    C:0.19536    A:0.34768    G:0.12252

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      25 | Ser S TCT       8 | Tyr Y TAT      25 | Cys C TGT       5
      TTC      17 |       TCC       7 |       TAC       8 |       TGC       7
Leu L TTA      20 |       TCA      16 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG       6 |       TAG       0 | Trp W TGG       5
------------------------------------------------------------------------------
Leu L CTT      20 | Pro P CCT       8 | His H CAT       4 | Arg R CGT       0
      CTC       4 |       CCC      10 |       CAC      12 |       CGC       3
      CTA       8 |       CCA      15 | Gln Q CAA      46 |       CGA       7
      CTG       5 |       CCG       4 |       CAG       8 |       CGG       3
------------------------------------------------------------------------------
Ile I ATT      50 | Thr T ACT      18 | Asn N AAT      53 | Ser S AGT      14
      ATC      11 |       ACC      17 |       AAC      27 |       AGC       6
      ATA      27 |       ACA      33 | Lys K AAA      37 | Arg R AGA       7
Met M ATG      17 |       ACG      12 |       AAG      13 |       AGG       5
------------------------------------------------------------------------------
Val V GTT      13 | Ala A GCT      16 | Asp D GAT      30 | Gly G GGT       6
      GTC       8 |       GCC       3 |       GAC      26 |       GGC       4
      GTA       8 |       GCA      11 | Glu E GAA      43 |       GGA      14
      GTG       4 |       GCG       9 |       GAG       5 |       GGG       6
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.17824    C:0.18171    A:0.40162    G:0.23843
position  2:    T:0.28009    C:0.22338    A:0.39005    G:0.10648
position  3:    T:0.34144    C:0.19676    A:0.33796    G:0.12384

Codon frequencies under model, for use in evolver:
  0.01772869  0.01021653  0.01754840  0.00643041
  0.01413900  0.00814790  0.01399521  0.00512838
  0.02468830  0.01422716  0.00000000  0.00000000
  0.00673983  0.00388397  0.00000000  0.00244462
  0.01807405  0.01041556  0.01789025  0.00655567
  0.01441443  0.00830662  0.01426784  0.00522829
  0.02516924  0.01450431  0.02491328  0.00912918
  0.00687113  0.00395963  0.00680125  0.00249224
  0.03994711  0.02302037  0.03954087  0.01448929
  0.03185865  0.01835922  0.03153466  0.01155551
  0.05562883  0.03205729  0.05506311  0.02017724
  0.01518651  0.00875155  0.01503207  0.00550833
  0.02371500  0.01366627  0.02347383  0.00860171
  0.01891320  0.01089913  0.01872086  0.00686004
  0.03302461  0.01903113  0.03268876  0.01197842
  0.00901562  0.00519544  0.00892394  0.00327007



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                 
Shig4337             0.4889 (0.1240 0.2536)
O157                 0.5266 (0.0695 0.1319) 0.3901 (0.1146 0.2937)


TREE #  1:  ((1, 2), 3);   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  4  np:  9):  -1871.752782     +0.000000
   4..5     5..1     5..2     4..3  
  0.05552  0.23720  0.73812  0.19195  4.04599  0.54756  0.43281  0.13590 47.69026
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.22280

((1: 0.237203, 2: 0.738124): 0.055521, 3: 0.191949);

((K12: 0.237203, Shig4337: 0.738124): 0.055521, O157: 0.191949);

Detailed output identifying parameters

kappa (ts/tv) =  4.04599


dN/dS for site classes (K=3)

p:   0.54756  0.43281  0.01963
w:   0.13590  1.00000 47.69026

dN & dS for each branch

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

   4..5       0.056    235.2    670.8   1.4432   0.0201   0.0139    3.3   13.5
   5..1       0.237    235.2    670.8   1.4432   0.0859   0.0595   14.0   57.6
   5..2       0.738    235.2    670.8   1.4432   0.2674   0.1853   43.6  179.3
   4..3       0.192    235.2    670.8   1.4432   0.0695   0.0482   11.3   46.6


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

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

   249 G      0.767         36.816
   296 S      0.608         29.377
   297 G      0.690         33.189
   301 L      0.996**       47.497
   302 G      0.874         41.786


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

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

   112 S      0.672         5.633 +- 3.833
   149 S      0.542         4.588 +- 3.860
   211 T      0.677         5.652 +- 3.814
   225 G      0.539         4.556 +- 3.853
   249 G      0.668         5.625 +- 3.852
   294 R      0.555         4.731 +- 3.913
   296 S      0.637         5.376 +- 3.883
   297 G      0.791         6.533 +- 3.527
   298 E      0.714         5.881 +- 3.692
   301 L      0.973*        7.792 +- 2.476
   302 G      0.717         6.002 +- 3.759



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:   0.116  0.206  0.302  0.289  0.083  0.005  0.000  0.000  0.000  0.000
w2:   0.012  0.025  0.036  0.053  0.077  0.104  0.132  0.160  0.188  0.215

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.039
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.022 0.108
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.058 0.124
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.006 0.086 0.115
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.004 0.009 0.108 0.094
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.005 0.012 0.117 0.071

sum of density on p0-p1 =   1.000000
