
seed used = 139994157

K12                                  ATG CGC TAC AGC AAA TTG ACA ATG CTT ATC CCC TGC GCA CTG CTC CTC AGT GCC TGC ACC ACA GTC ACT CCA GCT TAT AAA GAT AAC GGC ACA CGC AGT GGT CCT TGC GTT GAA GGA GGC CCG GAT AAC GTG GCC CAG CAA TTT TAT GAC TAC CGC ATT TTG CAC CGC AGC AAC GAC ATC ACC GCC TTG CGC CCT TAT CTG AGC GAC AAA CTG GCG ACA CTG CTT AGC GAT GCC TCC CGG GAT AAT AAC CAT CGG GAA CTA CTG ACC AAC GAT CCA TTC TCC AGT CGA ACC ACC TTG CCA GAT AGC GCC CAC GTT GCC AGT GCA TCG ACT ATC CCT AAT CGT GAT GCC CGT AAC ATT CCA TTG CGC GTG GAT CTC AAA CAG GGT GAC CAG GGT TGG CAG GAT GAA GTG TTA ATG ATT CAG GAA GGC CAG TGT TGG GTC ATC GAC GAT GTG CGT TAC TTA GGC GGT AGC GTT CAT GCC ACG GCG GGT ACG CTC CGT CAG TCC ATC GAG AAT CGC 
S2457T                               ATG CGC TAC CGT TCA CTA TCT CTA CTT ATT CCA TGT GCA CTG CTG CTG AGT GCC TGT ACC ACC GTC ACG CCA GCT TAT AAA GAT AAC GGC CCC CGC ACC GGT TCC TGT GTC CAG GGA GGG CCT GAC AGT GTG GCT CAA CAA TTC TAC GAC TAC CGC ATT CAA CAT CGC AGC AAT GAC ATT ACC GCC CTG CGC CCC TAT TTG AGT GAC AAA CTG GCA ACC CAA CTT AGC GAT GCC AGC CGC GAT AAT AGT CAT CGT GAA TTG TTA AGC AGC GAT CCG TTC TCC AGT CGA ACC ACC TTG CCA GAC AGC GCC CAC GTT GCC AGT GCA TCG ACT ATC CCT AAT CGT GAT GCC CGT AAC ATT CCA TTG CGG GTG GAT CTC AAA CAG GGT GAC CAG GGC TGG CAG GAT GAA GTG TTA ATG ATT CAG GAA GGC CAG TGT TGG GTC ATC GAC GAT GTG CGC TAC TTA GGC GGT AGC GTT CAT GCC ACG GCG GGT ACG CTC CGT CAG TCC ATC GAG AAT CGC 
Shig4337                             ATG CGC TAC CGT TCA CTA TCT CTA CTT ATT CCA TGT GCA CTG CTG CTG AGT GCC TGT ACC ACC GTC ACG CCA GCT TAT AAA GAT AAC GGC CCC CGC ACC GGT TCC TGT GTC CAG GGA GGG CCT GAC AGT GTG GCT CAA CAA TTC TAC GAC TAC CGC ATT CAA CAT CGC AGC AAT GAC ATT ACC GCC CTG CGC CCC TAT TTG AGT GAC AAA CTG GCA ACC CAA CTT AGC GAT GCC AGC CGC GAT AAT AGT CAT CGT GAA TTG TTA AGC AGC GAT CCG TTC TCC AGT CGA ACC ACC TTG CCA GAC AGC GCC CAC GTT GCC AGT GCA TCG ACT ATC CCT AAT CGT GAT GCC CGT AAC ATT CCA TTG CGG GTG GAT CTC AAA CAG GGT GAC CAG GGC TGG CAG GAT GAA GTG TTA ATG ATT CAG GAA GGC CAG TGT TGG GTC ATC GAC GAT GTG CGC TAC TTA GGC GGT AGC GTT CAT GCC ACG GCG GGT ACG CTC CGT CAG TCC ATC GAG AAT CGC 
CFT073                               ATG CGC TAT AGC AAA TTG ACC ATG CTT ATC CCT TGC GCA CTG CTA CTC AGT GCC TGT ACC ACC GTC ACG CCA GCT TAT AAA GAT AAC GGC CCC CGC ACC GGT TCC TGT GTC CAG GGG GGG CCT GAT AGC GTG GCT CAA CAG TTC TAT GAC TAC CGC ATT CAA CAT CGC GGC AAT GAC ATT ACC GCT CTG CGC CCC TAT TTG AGT GAC AAA CTG GCA ACC CTA CTT AGC GAT GCC AGC CGC GAT AAT AGT CAT CGT GAA TTG TTA AGC AGC GAT CCG TTC TCC AGT CGA ACC ACC TTG CCA GAC AGC GCC CAC GTT GCC AGT GCA TCT ACT ATC CCT AAT CGT GAT GCC CGT AAC ATT CCA TTG CGC GTG GAT CTC AAG CAG GGT GAC CAG GGC TGG CAG GAT GAA GTG TTA ATG ATT CAG GAA GGC CAG TGT TGG GTC ATC GAC GAT GTG CGC TAC TTA GGC GGT AGC GTT CAT GCC ACG GCG GGT ACG CTC CGT CAG TCC ATC GAG AAT CGC 
O157                                 ATG CGC TAC CGT TCA CTA TCT CTA CTT ATT CCA TGT GCA CTG CTG CTG AGT GCC TGT ACC ACC GTC ACG CCA GCT TAT AAA GAT AAT GGT CCC CGC ACC GGT TCC TGT GTC CAG GGG GGG CCT GAC AGC GTG GCC CAA CAA TTC TAT GAC TAC CAC ATT CAA CAT CGC AGC AAT GAC ATT ACC GCC CTG CGC CCC TAT TTG AGT GAC AAA CTG GCA ACC CTA CTT AGC GAT GCC AGC CGC GAT AAT AGT CAT CGT GAA TTG TTA AGC AGT GAT CCG TTC TCC AGT CGA ACC ACC TTG CCA GAC AGC GCC CAC GTT GCC AGT GCA TCG ACT ATC CCT AAT CGT GAT GCC CGT AAC ATT CCA TTG CGC GTG GAT CTC AAG CAG GGT GAC CAG GGC TGG CAG GAT GAA GTG TTA ATG ATT CAG GAA GGC CAG TGT TGG GTG ATC GAC GAT GTG CGC TAC TTA GGC GGT AGC GTT CAT GCC ACG GCG GGT ACG CTC CGT CAG TCC ATC GAG AAT CGC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0865.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 171
# site patterns = 103
    2    5    1    1    1    1    1    1    2    1    1    1    2    2    1
    1    3    6    2    4    2    1    1    3    1    2    2    8    1    1
    1    1    4    1    1    1    1    1    1    1    1    4    1    1    1
    1    1    5    2    1    3    1    1    1    1    1    1    1    1    1
    1    1    1    3    1    1    3    1    2    1    3    1    1    1    1
    1    1    2    1    2    1    1    2    1    1    3    1    3    1    1
    2    1    6    1    2    2    2    1    1    1    2    1    1

1       
K12                   ATG CGC TAC AGC AAA TTG ACA ATG CTT ATC CCC TGC GCA CTG CTC CTC AGT GCC TGC ACC ACA GTC ACT CCA GCT TAT AAA GAT AAC GGC ACA AGT GGT CCT GTT GAA GGA GGC CCG GAT AAC GTG GCC CAG CAA TTT TAT GAC TAC CGC ATT TTG CAC AGC AAC ATC GCC TTG CCT CTG AGC GCG CTG AGC TCC CGG AAT AAC CAT CGG GAA CTA CTG ACC AAC CCA TTC TCC CGA TTG GAT CAC GTT TCG ACT ATC CCT CGT AAC CGC CTC AAA CAG GGT TGG TTA GGC TGT GTC CGT ACG GCG GAG 
S2457T                ... ... ... C.T TC. C.A T.T C.A ... ..T ..A ..T ... ... ..G ..G ... ... ..T ... ..C ... ..G ... ... ... ... ... ... ... C.C .CC ... T.C ..C C.G ... ..G ..T ..C .GT ... ..T ..A ... ..C ..C ... ... ... ... CAA ..T ... ..T ..T ... C.. ..C T.. ..T ..A .AA ... AG. ..C ... .GT ... ..T ... T.G T.A .G. .G. ..G ... ... ... ... ..C ... ... ... ... ... ... ... ... ..G ... ... ... ..C ... ... ... ... ... ..C ... ... ... 
Shig4337              ... ... ... C.T TC. C.A T.T C.A ... ..T ..A ..T ... ... ..G ..G ... ... ..T ... ..C ... ..G ... ... ... ... ... ... ... C.C .CC ... T.C ..C C.G ... ..G ..T ..C .GT ... ..T ..A ... ..C ..C ... ... ... ... CAA ..T ... ..T ..T ... C.. ..C T.. ..T ..A .AA ... AG. ..C ... .GT ... ..T ... T.G T.A .G. .G. ..G ... ... ... ... ..C ... ... ... ... ... ... ... ... ..G ... ... ... ..C ... ... ... ... ... ..C ... ... ... 
CFT073                ... ... ..T ... ... ... ..C ... ... ... ..T ... ... ... ..A ... ... ... ..T ... ..C ... ..G ... ... ... ... ... ... ... C.C .CC ... T.C ..C C.G ..G ..G ..T ... .G. ... ..T ..A ..G ..C ... ... ... ... ... CAA ..T G.. ..T ..T ..T C.. ..C T.. ..T ..A ..A ... AG. ..C ... .GT ... ..T ... T.G T.A .G. .G. ..G ... ... ... ... ..C ... ... ..T ... ... ... ... ... ... ... ..G ... ..C ... ... ... ... ... ..C ... ... ... 
O157                  ... ... ... C.T TC. C.A T.T C.A ... ..T ..A ..T ... ... ..G ..G ... ... ..T ... ..C ... ..G ... ... ... ... ... ..T ..T C.C .CC ... T.C ..C C.G ..G ..G ..T ..C .G. ... ... ..A ... ..C ... ... ... .A. ... CAA ..T ... ..T ..T ... C.. ..C T.. ..T ..A ..A ... AG. ..C ... .GT ... ..T ... T.G T.A .G. .GT ..G ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ..G ... ..C ... ... ... ... ..G ..C ... ... ... 

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

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

#1: K12            
position  1:    T:0.14620    C:0.27485    A:0.27485    G:0.30409
position  2:    T:0.23977    C:0.22807    A:0.29825    G:0.23392
position  3:    T:0.27485    C:0.38012    A:0.14035    G:0.20468

#2: S2457T         
position  1:    T:0.15789    C:0.29240    A:0.25146    G:0.29825
position  2:    T:0.22807    C:0.22807    A:0.28655    G:0.25731
position  3:    T:0.29825    C:0.36257    A:0.14620    G:0.19298

#3: Shig4337       
position  1:    T:0.15789    C:0.29240    A:0.25146    G:0.29825
position  2:    T:0.22807    C:0.22807    A:0.28655    G:0.25731
position  3:    T:0.29825    C:0.36257    A:0.14620    G:0.19298

#4: CFT073         
position  1:    T:0.15205    C:0.27485    A:0.26901    G:0.30409
position  2:    T:0.23392    C:0.22222    A:0.28655    G:0.25731
position  3:    T:0.30409    C:0.38012    A:0.11696    G:0.19883

#5: O157           
position  1:    T:0.15789    C:0.29240    A:0.25146    G:0.29825
position  2:    T:0.23392    C:0.22807    A:0.28655    G:0.25146
position  3:    T:0.30994    C:0.35088    A:0.13450    G:0.20468

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       1 | Ser S TCT       4 | Tyr Y TAT      14 | Cys C TGT      16
      TTC       9 |       TCC      15 |       TAC      16 |       TGC       4
Leu L TTA      14 |       TCA       3 | *** * TAA       0 | *** * TGA       0
      TTG      22 |       TCG       4 |       TAG       0 | Trp W TGG      10
------------------------------------------------------------------------------
Leu L CTT      10 | Pro P CCT      12 | His H CAT      14 | Arg R CGT      23
      CTC      13 |       CCC       9 |       CAC       7 |       CGC      40
      CTA      10 |       CCA      19 | Gln Q CAA      14 |       CGA       5
      CTG      23 |       CCG       5 |       CAG      36 |       CGG       4
------------------------------------------------------------------------------
Ile I ATT      22 | Thr T ACT       6 | Asn N AAT      20 | Ser S AGT      27
      ATC      18 |       ACC      34 |       AAC      13 |       AGC      35
      ATA       0 |       ACA       4 | Lys K AAA      15 | Arg R AGA       0
Met M ATG      12 |       ACG      14 |       AAG       2 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      11 | Ala A GCT       9 | Asp D GAT      43 | Gly G GGT      22
      GTC      13 |       GCC      36 |       GAC      32 |       GGC      20
      GTA       0 |       GCA      14 | Glu E GAA      16 |       GGA       3
      GTG      21 |       GCG       6 |       GAG       5 |       GGG       6
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15439    C:0.28538    A:0.25965    G:0.30058
position  2:    T:0.23275    C:0.22690    A:0.28889    G:0.25146
position  3:    T:0.29708    C:0.36725    A:0.13684    G:0.19883

Codon frequencies under model, for use in evolver:
  0.01089587  0.01346970  0.00501896  0.00729251
  0.01062211  0.01313127  0.00489286  0.00710928
  0.01352402  0.01671867  0.00000000  0.00000000
  0.01177192  0.01455269  0.00000000  0.00787885
  0.02014086  0.02489854  0.00927748  0.01348010
  0.01963480  0.02427295  0.00904438  0.01314140
  0.02499895  0.03090422  0.01151526  0.01673158
  0.02176022  0.02690043  0.01002341  0.01456393
  0.01832488  0.02265359  0.00844099  0.01226468
  0.01786445  0.02208440  0.00822890  0.01195652
  0.02274495  0.02811777  0.01047700  0.01522300
  0.01979823  0.02447498  0.00911966  0.01325079
  0.02121393  0.02622510  0.00977177  0.01419830
  0.02068092  0.02556618  0.00952625  0.01384156
  0.02633086  0.03255075  0.01212878  0.01762302
  0.02291958  0.02833365  0.01055744  0.01533987



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               0.0785 (0.0463 0.5902)
Shig4337             0.0785 (0.0463 0.5902)-1.0000 (0.0000 0.0000)
CFT073               0.0600 (0.0314 0.5223) 0.1089 (0.0195 0.1788) 0.1089 (0.0195 0.1788)
O157                 0.0739 (0.0463 0.6273) 0.0604 (0.0052 0.0854) 0.0604 (0.0052 0.0854) 0.1088 (0.0195 0.1789)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 77
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1070.574037     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00022  0.71252  0.03419  0.00000  0.00000  0.01075  0.17410  0.04534  2.54797  0.94519  0.03652  0.03987 11.50310
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.97713

((1: 0.712517, (2: 0.000004, 3: 0.000004): 0.034192): 0.000223, (4: 0.174102, 5: 0.045336): 0.010750);

((K12: 0.712517, (S2457T: 0.000004, Shig4337: 0.000004): 0.034192): 0.000223, (CFT073: 0.174102, O157: 0.045336): 0.010750);

Detailed output identifying parameters

kappa (ts/tv) =  2.54797


dN/dS for site classes (K=3)

p:   0.94519  0.03652  0.01828
w:   0.03987  1.00000 11.50310

dN & dS for each branch

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

   6..7       0.000    136.1    376.9   0.2845   0.0000   0.0002    0.0    0.0
   7..1       0.713    136.1    376.9   0.2845   0.1425   0.5007   68.1   53.7
   7..8       0.034    136.1    376.9   0.2845   0.0068   0.0240    3.3    2.6
   8..2       0.000    136.1    376.9   0.2845   0.0000   0.0000    0.0    0.0
   8..3       0.000    136.1    376.9   0.2845   0.0000   0.0000    0.0    0.0
   6..9       0.011    136.1    376.9   0.2845   0.0021   0.0076    1.0    0.8
   9..4       0.174    136.1    376.9   0.2845   0.0348   0.1223   16.7   13.1
   9..5       0.045    136.1    376.9   0.2845   0.0091   0.0319    4.3    3.4


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

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

     5 K      0.998**       11.478
     7 T      0.559         6.843
     8 M      0.894         10.385


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

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

     4 S      0.501         4.161 +- 3.679
     5 K      0.996**       7.615 +- 2.180
     7 T      0.718         5.736 +- 3.541
     8 M      0.931         7.205 +- 2.668



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:   1.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.003  0.016  0.042  0.075  0.106  0.131  0.148  0.158  0.162  0.160

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 0.000
 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 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005
 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 0.013 0.983

sum of density on p0-p1 =   1.000000
