
seed used = 139997785

K12                                  ATG AAT ATG AAG ACC ATT GAA GAT GTA TTT ATT CAC CTG CTT TCA GAT ACC TAC AGC GCA GAA AAA CAA TTA ACC CGG GCA CTG GCA AAA CTC GCA AGA GCA ACA TCA AAT GAA AAA TTA AGT CAG GCT TTT CAT GCG CAC CTC GAG GAA ACT CAT GGA CAG ATT GAA CGT ATT GAT CAA GTT GTG GAG TCC GAA TCG AAC CTG AAA ATT AAG CGC ATG AAA TGT GTG GCA ATG GAA GGT CTT ATT GAA GAA GCT AAT GAG GTC ATC GAA AGT ACC GAG AAA AAC GAA GTG CGT GAT GCC GCA CTG ATT GCC GCA GCA CAG AAA GTC GAG CAT TAT GAG ATT GCC AGT TAC GGG ACA TTA GCG ACG CTG GCT GAA CAA TTA GGT TAC CGT AAA GCA GCG AAG CTT CTG AAA GAA ACC CTG GAA GAA GAA AAG GCC ACC GAC ATC AAA CTG ACT GAT CTG GCC ATT AAT AAC GTA AAT AAG AAA GCC GAA AAT AAA GCC 
S2457T                               ATG AAT ATG AAG ACC ATT GAA GAT GTA TTT ATT CAA CTG CTT TCA GAT ACC TAC AGC GCA GAA AAA CAA TTA ACC CGG GCA CTG GCA AAA CTC GCA AGA GCA ACA TCA AAT GAA AAA TTA AGT CAG GCT TTT CAT GCG CAC CTC GAG GAA ACT CAT GGA CAG ATT GAA CGA ATT GAT CAA GTT GTG GAA TCA GAA TCA AAT CTG AAA ATT AAG CGC ATG AAA TGT GTG GCA ATG GAA GGT CTT ATT GAA GAA GCT AAT GAG GTC ATC GAA AGT ACC GAG AAA AAC GAA GTG CGT GAT GCC GCA CTG ATT GCC GCA GCA CAG AAA GTC GAG CAT TAT GAG ATT GCC AGT TAC GGG ACA TTA GCG ACG CTG GCT GAA CAA TTA GGT TAC CGT AAA GCA GCG AAG CTT CTG AAA GAA ACC CTG GAA GAA GAA AAG GCC ACC GAC ATC AAA CTG ACT GAT CTG GCC CTT AAT AAC GTA AAT AAG AAA GCC GAA AAT AAA GCC 
Shig4337                             ATG AAT ATG AAG ACC ATT GAA GAT GTA TTT ATT CAA CTG CTT TCA GAT ACC TAC AGC GCA GAA AAA CAA TTA ACC CGG GCA CTG GCA AAA CTC GCA AGA GCA ACA TCA AAT GAA AAA TTA AGT CAG GCT TTT CAT GCG CAC CTC GAG GAA ACT CAT GGA CAG ATT GAA CGA ATT GAT CAA GTT GTG GAA TCA GAA TCA AAT CTG AAA ATT AAG CGC ATG AAA TGT GTG GCA ATG GAA GGT CTT ATT GAA GAA GCT AAT GAG GTC ATC GAA AGT ACC GAG AAA AAC GAA GTG CGT GAT GCC GCA CTG ATT GCC GCA GCA CAG AAA GTC GAG CAT TAT GAG ATT GCC AGT TAC GGG ACA TTA GCG ACG CTG GCT GAA CAA TTA GGT TAC CGT AAA GCA GCG AAG CTT CTG AAA GAA ACC CTG GAA GAA GAA AAG GCC ACC GAC ATC AAA CTG ACT GAT CTG GCC CTT AAT AAC GTA AAT AAG AAA GCC GAA AAT AAA GCC 
CFT073                               TCG ACA CAC AAC ACT CAT ATT AAT GAA ACT ATT CAC CTG CTT TCA GAT ACA TAC AGC GCA GAA AAA CAA TTA ACC CGG GCG CTG GCA AAA CTC GCA AGA GCA ACA TCA AAC GAA AAA TTA AGT CAG GCT TTT CAT GCG CAC CTC GAG GAA ACA CAT GGA CAG ATT GAA CGT ATT GAT CAA ATT GTG GAA TCA GAA TCG AAT CTG AAA ATT AAG CGC ATG AAA TGT GTG GCA ATG GAA GGT CTT ATT GAA GAA GCT GAT GAG GTC ATC GAA AGT ACC GAG AAA AAC GAA GTG CGT GAT GCC GCA CTG ATT GCC GCA GCA CAG AAA GTC GAG CAT TAT GAG ATT GCC AGT TAC GGG ACA TTA GCG ACG CTG GCT GAA CAA TTA GGT TAT CGT AAA GCA GCG AAG CTT CTG AAA GAT ACC CTG GAA GAA GAA AAG GCC ACC GAC ATC AAA TTG ACT GAT CTG GCC CTT AAT AAC GTA AAT AAG AAA GCC GAA AAT AAA GCC 
O157                                 ATG AAT ATG AAG ACC ATT GAA GAT GTA TTT ATT CAC CTG CTT TCA GAT ACC TAC AGC GCA GAA AAA CAA TTA ACC CGG GCA CTG GCA AAA CTC GCA AGA GCA ACA TCA AAC GAA AAA TTA AGT CAG GCT TTT CAT GCG CAC CTC GAG GAA ACA CAT GGA CAG ATT GAA CGT ATT GAT CAA GTT GTG GAA TCA GAA TCG AAT CTG AAA ATT AAG CGC ATG AAA TGT GTG GCA ATG GAA GGT CTT ATT GAA GAA GCT AAT GAG GTC ATC GAA AGT ACC GAG AAA AAC GAA GTG CGT GAT GCC GCA CTG ATT GCC GCA GCA CAG AAA GTC GAG CAT TAT GAG ATT GCC AGT TAC GGG ACA TTA GCG ACG CTG GCT GAA CAA TTA GGT TAC CGT AAA GCA GCG AAG CTT CTG AAA GAG ACC CTG GAA GAA GAA AAG GCC ACC GAC ATC AAA CTG ACT GAT CTG GCC CTT AAT AAC GTA AAT AAG AAA GCC GAA AAT AAA GCC 
EDL933                               ATG AAT ATG AAG ACC ATT GAA GAT GTA TTT ATT CAC CTG CTT TCA GAT ACC TAC AGC GCA GAA AAA CAA TTA ACC CGG GCA CTG GCA AAA CTC GCA AGA GCA ACA TCA AAC GAA AAA TTA AGT CAG GCT TTT CAT GCG CAC CTC GAG GAA ACA CAT GGA CAG ATT GAA CGT ATT GAT CAA GTT GTG GAA TCA GAA TCG AAT CTG AAA ATT AAG CGC ATG AAA TGT GTG GCA ATG GAA GGT CTT ATT GAA GAA GCT AAT GAG GTC ATC GAA AGT ACC GAG AAA AAC GAA GTG CGT GAT GCC GCA CTG ATT GCC GCA GCA CAG AAA GTC GAG CAT TAT GAG ATT GCC AGT TAC GGG ACA TTA GCG ACG CTG GCT GAA CAA TTA GGT TAC CGT AAA GCA GCG AAG CTT CTG AAA GAG ACC CTG GAA GAA GAA AAG GCC ACC GAC ATC AAA CTG ACT GAT CTG GCC CTT AAT AAC GTA AAT AAG AAA GCC GAA AAT AAA GCC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1258.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 166
# site patterns = 70
    1    1    1    1    1    1    1    1    1    1    7    1    8    3    2
    4    1    2    1    9   15   12    3    4    4    1    1    2    1    2
    1    3    3    3    1    3    3    1    5    1    1    1    1    3    1
    1    1    1    4    1    2    1    2    1    2    2    2    2    7    1
    1    1    1    1    1    1    1    1    3    1

1       
K12                   ATG AAT ATG AAG ACC ATT GAA GAT GTA TTT ATT CAC CTG CTT TCA GAT ACC TAC AGC GCA GAA AAA CAA TTA ACC CGG GCA CTC AGA ACA AAT AGT CAG GCT TTT CAT GCG CAC GAG ACT GGA CGT GTT GTG GAG TCC TCG AAC AAG CGC ATG TGT GGT AAT GTC ATC AAC CGT GCC TAT GGG ACG TAC GAA GAC CTG ACT ATT AAT GTA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..A ..A ..A ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..A ..A ..A ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... 
CFT073                TC. .CA CAC ..C ..T CA. ATT A.. .A. AC. ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ..G ... ... ... ..C ... ... ... ... ... ... ... ... ..A ... ... A.. ... ..A ..A ... ..T ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ..T ..T ... T.. ... C.. ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ..A ... ... ... ... ..A ..A ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... C.. ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ..A ... ... ... ... ..A ..A ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... C.. ... ... 

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

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

#1: K12            
position  1:    T:0.09036    C:0.18072    A:0.34337    G:0.38554
position  2:    T:0.25904    C:0.22892    A:0.42169    G:0.09036
position  3:    T:0.26506    C:0.18675    A:0.32530    G:0.22289

#2: S2457T         
position  1:    T:0.09036    C:0.18675    A:0.33735    G:0.38554
position  2:    T:0.25904    C:0.22892    A:0.42169    G:0.09036
position  3:    T:0.26506    C:0.16867    A:0.35542    G:0.21084

#3: Shig4337       
position  1:    T:0.09036    C:0.18675    A:0.33735    G:0.38554
position  2:    T:0.25904    C:0.22892    A:0.42169    G:0.09036
position  3:    T:0.26506    C:0.16867    A:0.35542    G:0.21084

#4: CFT073         
position  1:    T:0.09639    C:0.19277    A:0.33735    G:0.37349
position  2:    T:0.23494    C:0.24699    A:0.42771    G:0.09036
position  3:    T:0.27711    C:0.17470    A:0.33735    G:0.21084

#5: O157           
position  1:    T:0.09036    C:0.18675    A:0.33735    G:0.38554
position  2:    T:0.25904    C:0.22892    A:0.42169    G:0.09036
position  3:    T:0.25904    C:0.18072    A:0.33735    G:0.22289

#6: EDL933         
position  1:    T:0.09036    C:0.18675    A:0.33735    G:0.38554
position  2:    T:0.25904    C:0.22892    A:0.42169    G:0.09036
position  3:    T:0.25904    C:0.18072    A:0.33735    G:0.22289

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      11 | Ser S TCT       0 | Tyr Y TAT       7 | Cys C TGT       6
      TTC       0 |       TCC       1 |       TAC      17 |       TGC       0
Leu L TTA      24 |       TCA      19 | *** * TAA       0 | *** * TGA       0
      TTG       1 |       TCG       5 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT      23 | Pro P CCT       0 | His H CAT      19 | Arg R CGT      16
      CTC      12 |       CCC       0 |       CAC      11 |       CGC       6
      CTA       0 |       CCA       0 | Gln Q CAA      20 |       CGA       2
      CTG      53 |       CCG       0 |       CAG      18 |       CGG       6
------------------------------------------------------------------------------
Ile I ATT      50 | Thr T ACT      11 | Asn N AAT      37 | Ser S AGT      18
      ATC      12 |       ACC      34 |       AAC      17 |       AGC       6
      ATA       0 |       ACA      17 | Lys K AAA      72 | Arg R AGA       6
Met M ATG      22 |       ACG       6 |       AAG      29 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       5 | Ala A GCT      18 | Asp D GAT      31 | Gly G GGT      12
      GTC      12 |       GCC      42 |       GAC       6 |       GGC       0
      GTA      11 |       GCA      59 | Glu E GAA     104 |       GGA       6
      GTG      18 |       GCG      19 |       GAG      33 |       GGG       6
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.09137    C:0.18675    A:0.33835    G:0.38353
position  2:    T:0.25502    C:0.23193    A:0.42269    G:0.09036
position  3:    T:0.26506    C:0.17671    A:0.34137    G:0.21687

Codon frequencies under model, for use in evolver:
  0.00633022  0.00422015  0.00815256  0.00517927
  0.00575701  0.00383801  0.00741433  0.00471028
  0.01049222  0.00699481  0.00000000  0.00000000
  0.00224299  0.00149533  0.00000000  0.00183518
  0.01293870  0.00862580  0.01666347  0.01058621
  0.01176708  0.00784472  0.01515457  0.00962761
  0.02144563  0.01429709  0.02761938  0.01754643
  0.00458458  0.00305638  0.00590438  0.00375102
  0.02344269  0.01562846  0.03019134  0.01918038
  0.02131993  0.01421328  0.02745748  0.01744358
  0.03885580  0.02590386  0.05004156  0.03179111
  0.00830646  0.00553764  0.01069772  0.00679620
  0.02657302  0.01771535  0.03422283  0.02174156
  0.02416680  0.01611120  0.03112391  0.01977284
  0.04404426  0.02936284  0.05672366  0.03603621
  0.00941564  0.00627709  0.01212620  0.00770370



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               0.1164 (0.0052 0.0450)
Shig4337             0.1164 (0.0052 0.0450)-1.0000 (0.0000 0.0000)
CFT073               0.5147 (0.0536 0.1042) 0.5728 (0.0537 0.0938) 0.5728 (0.0537 0.0938)
O157                 0.0480 (0.0026 0.0544) 0.0583 (0.0026 0.0449) 0.0583 (0.0026 0.0449) 0.9146 (0.0509 0.0556)
EDL933               0.0480 (0.0026 0.0544) 0.0583 (0.0026 0.0449) 0.0583 (0.0026 0.0449) 0.9146 (0.0509 0.0556)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 27
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -824.649641     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.01474  0.02439  0.01825  0.00000  0.00000  0.00375  0.19135  0.00000  0.00000  0.00000  1.23713  0.92001  0.00000  0.09681  6.18093
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.25250

((1: 0.024390, (2: 0.000004, 3: 0.000004): 0.018255): 0.014736, (4: 0.191347, (5: 0.000004, 6: 0.000004): 0.000000): 0.003752);

((K12: 0.024390, (S2457T: 0.000004, Shig4337: 0.000004): 0.018255): 0.014736, (CFT073: 0.191347, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.003752);

Detailed output identifying parameters

kappa (ts/tv) =  1.23713


dN/dS for site classes (K=3)

p:   0.92001  0.00000  0.07999
w:   0.09681  1.00000  6.18093

dN & dS for each branch

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

   7..8       0.015    115.5    382.5   0.5835   0.0042   0.0072    0.8    1.6
   8..1       0.024    115.5    382.5   0.5835   0.0070   0.0120    1.4    2.7
   8..9       0.018    115.5    382.5   0.5835   0.0052   0.0089    1.0    2.0
   9..2       0.000    115.5    382.5   0.5835   0.0000   0.0000    0.0    0.0
   9..3       0.000    115.5    382.5   0.5835   0.0000   0.0000    0.0    0.0
   7..10      0.004    115.5    382.5   0.5835   0.0011   0.0018    0.2    0.4
  10..4       0.191    115.5    382.5   0.5835   0.0547   0.0938   10.8   20.9
  10..11      0.000    115.5    382.5   0.5835   0.0000   0.0000    0.0    0.0
  11..5       0.000    115.5    382.5   0.5835   0.0000   0.0000    0.0    0.0
  11..6       0.000    115.5    382.5   0.5835   0.0000   0.0000    0.0    0.0


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

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

     1 M      0.991**       6.128
     2 N      0.909         5.629
     3 M      1.000**       6.179
     6 I      0.989*        6.113
     7 E      0.998**       6.166
     9 V      0.501         3.142
    10 F      0.993**       6.138
    12 H      0.577         3.609
    61 V      0.588         3.675
   155 I      0.657         4.095


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

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

     1 M      0.852         6.291 +- 3.031
     2 N      0.639         4.773 +- 3.506
     3 M      0.965*        7.033 +- 2.444
     6 I      0.822         6.085 +- 3.132
     7 E      0.915         6.705 +- 2.738
    10 F      0.875         6.456 +- 2.937



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:   0.599  0.302  0.082  0.014  0.002  0.000  0.000  0.000  0.000  0.000
w2:   0.005  0.025  0.058  0.093  0.123  0.143  0.151  0.147  0.135  0.119

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 0.001 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.007 0.028
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.041 0.091
 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 0.022 0.150 0.147
 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 0.003 0.017 0.081 0.276 0.121

sum of density on p0-p1 =   1.000000
