
seed used = 140004745

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2005.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 124
# site patterns = 83
    2    1    2    2    2    1    1    1    1    1    1    1    1    1    1
    3    1    1    1    1    1    5    1    7    1    1    1    3    1    1
    2    3    1    2    1    1    1    2    2    2    2    4    2    1    1
    1    1    1    1    2    3    1    1    2    2    1    1    4    1    1
    2    1    1    1    1    1    1    2    1    1    2    1    1    1    1
    1    1    1    1    1    1    1    1

1       
K12                   ATG AAA ACA TTA CCT GTA TTA CCC GGG CAG GCG GCC AGT TCT CGC CCG TCT GTT GAA ATC TGG CAG ATA CTG CTG TCC CGA GAC CAC TAT GGC CTC ACA AAT CCT TTT GCC GAT GAA CGT GTG ATT GAG CAT GCA GGC TCA TGT GAT GCG AAC TTT GTG AAA TAC GCG GTG ACC GGA TTC AGC GCC TGT ACC CGC TCT ATA ATC CGG GCT CGC AGG GCG GAC AAT AGA ACG GTA CTG GGT AAG TAT GAG 
S2457T                ... ..T ... ... ..C .AC ACT .A. .TA .G. .A. ..A TCG GGC T.. ... ... A.C ACC ... ... ... .C. ... ..C A.. ... ... ... ... ... ... ..G ... ..G ..C ..T ... ... ... ... ... ... ... ... ..A ... ... ..C ... ... ... ..T ... ... ... ..A ... ... ... ... ..A G.A G.. .CG ..G ..C ..T ... ..A ... C.. ..A ..T ..C ... ... ... .G. ..G ... C.. ..A 
Shig4337              ... ..T ... ... ..C .AC ACT .A. .TA .G. .A. ..A TCG GGC T.. ... ... A.C ACC ... ... ... .C. ... ..C A.. ... ... ... ... ... ... ..G ... ..G ..C ..T ... ... ... ... ... ... ... ... ..A ... ... ..C ... ... ... ..T ... ... ... ..A ... ... ... ... ..A G.A G.. .CG ..G ..C ..T ... ..A ... C.. ..A ..T ..C ... ... ... .G. ..G ... C.. ..A 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
O157                  ... ... ... ... ..C .AT AC. .A. .TA .G. .A. ..A TCG CGC T.. ... ... A.C ACC ... ... ... .C. ... ..T GG. ..T ... ... ..C ... ... ..G ... ..G ..C ..T ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... 

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

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

#1: K12            
position  1:    T:0.14516    C:0.28226    A:0.28226    G:0.29032
position  2:    T:0.29032    C:0.25000    A:0.28226    G:0.17742
position  3:    T:0.23387    C:0.29032    A:0.16935    G:0.30645

#2: S2457T         
position  1:    T:0.12097    C:0.29032    A:0.29032    G:0.29839
position  2:    T:0.26613    C:0.26613    A:0.29032    G:0.17742
position  3:    T:0.18548    C:0.31452    A:0.19355    G:0.30645

#3: Shig4337       
position  1:    T:0.12097    C:0.29032    A:0.29032    G:0.29839
position  2:    T:0.26613    C:0.26613    A:0.29032    G:0.17742
position  3:    T:0.18548    C:0.31452    A:0.19355    G:0.30645

#4: CFT073         
position  1:    T:0.14516    C:0.28226    A:0.28226    G:0.29032
position  2:    T:0.29032    C:0.25000    A:0.28226    G:0.17742
position  3:    T:0.21774    C:0.29839    A:0.16935    G:0.31452

#5: O157           
position  1:    T:0.12903    C:0.29032    A:0.29839    G:0.28226
position  2:    T:0.28226    C:0.24194    A:0.29032    G:0.18548
position  3:    T:0.20968    C:0.32258    A:0.15323    G:0.31452

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       7 | Ser S TCT      10 | Tyr Y TAT       5 | Cys C TGT       8
      TTC       8 |       TCC       2 |       TAC      12 |       TGC       3
Leu L TTA      12 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       5 |       TAG       0 | Trp W TGG       5
------------------------------------------------------------------------------
Leu L CTT       1 | Pro P CCT       5 | His H CAT       8 | Arg R CGT      11
      CTC      17 |       CCC       8 |       CAC       8 |       CGC      16
      CTA       0 |       CCA       0 | Gln Q CAA       0 |       CGA       4
      CTG      40 |       CCG      21 |       CAG      27 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      24 | Thr T ACT       2 | Asn N AAT      15 | Ser S AGT       2
      ATC      16 |       ACC      28 |       AAC      17 |       AGC      10
      ATA       5 |       ACA      16 | Lys K AAA      13 | Arg R AGA       5
Met M ATG      10 |       ACG       8 |       AAG       5 |       AGG       3
------------------------------------------------------------------------------
Val V GTT       4 | Ala A GCT       6 | Asp D GAT      16 | Gly G GGT       4
      GTC       0 |       GCC       9 |       GAC      22 |       GGC      15
      GTA      12 |       GCA      14 | Glu E GAA      14 |       GGA       9
      GTG      17 |       GCG      19 |       GAG      16 |       GGG       4
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.13226    C:0.28710    A:0.28871    G:0.29194
position  2:    T:0.27903    C:0.25484    A:0.28710    G:0.17903
position  3:    T:0.20645    C:0.30806    A:0.17581    G:0.30968

Codon frequencies under model, for use in evolver:
  0.00779509  0.01163174  0.00663801  0.01169264
  0.00711922  0.01062321  0.00606246  0.01067882
  0.00802038  0.01196792  0.00000000  0.00000000
  0.00500147  0.00746314  0.00000000  0.00750221
  0.01692105  0.02524938  0.01440933  0.02538158
  0.01545391  0.02306013  0.01315997  0.02318086
  0.01741010  0.02597913  0.01482579  0.02611515
  0.01085686  0.01620047  0.00924529  0.01628529
  0.01701611  0.02539123  0.01449028  0.02552417
  0.01554073  0.02318968  0.01323390  0.02331109
  0.01750791  0.02612508  0.01490908  0.02626186
  0.01091785  0.01629148  0.00929723  0.01637678
  0.01720624  0.02567493  0.01465219  0.02580936
  0.01571437  0.02344878  0.01338177  0.02357155
  0.01770353  0.02641698  0.01507566  0.02655529
  0.01103984  0.01647351  0.00940111  0.01655976



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               0.2216 (0.0955 0.4310)
Shig4337             0.2216 (0.0955 0.4310)-1.0000 (0.0000 0.0000)
CFT073               0.0000 (0.0000 0.0214) 0.2216 (0.0955 0.4310) 0.2216 (0.0955 0.4310)
O157                 0.4392 (0.0817 0.1859) 0.1128 (0.0332 0.2941) 0.1128 (0.0332 0.2941) 0.5130 (0.0817 0.1592)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 68
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):   -820.965591     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00096  0.00954  1.95632  0.00000  0.00000  0.00986  0.00000  0.85162  2.11818  0.78529  0.15472  0.00000 31.09277
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   2.82830

((1: 0.009542, (2: 0.000004, 3: 0.000004): 1.956316): 0.000955, (4: 0.000004, 5: 0.851619): 0.009857);

((K12: 0.009542, (S2457T: 0.000004, Shig4337: 0.000004): 1.956316): 0.000955, (CFT073: 0.000004, O157: 0.851619): 0.009857);

Detailed output identifying parameters

kappa (ts/tv) =  2.11818


dN/dS for site classes (K=3)

p:   0.78529  0.15472  0.06000
w:   0.00000  1.00000 31.09277

dN & dS for each branch

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

   6..7       0.001     98.6    273.4   2.0202   0.0004   0.0002    0.0    0.1
   7..1       0.010     98.6    273.4   2.0202   0.0037   0.0018    0.2    1.0
   7..8       1.956     98.6    273.4   2.0202   0.7529   0.3727   36.8  205.8
   8..2       0.000     98.6    273.4   2.0202   0.0000   0.0000    0.0    0.0
   8..3       0.000     98.6    273.4   2.0202   0.0000   0.0000    0.0    0.0
   6..9       0.010     98.6    273.4   2.0202   0.0038   0.0019    0.2    1.0
   9..4       0.000     98.6    273.4   2.0202   0.0000   0.0000    0.0    0.0
   9..5       0.852     98.6    273.4   2.0202   0.3278   0.1622   16.0   89.6


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

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

     6 V      0.937         29.194
     7 L      0.997**       31.011
     9 G      0.751         23.615
    13 S      1.000**       31.089
    14 S      0.998**       31.040
    20 E      0.998**       31.043
    27 S      0.811         25.409


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

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

     6 V      0.950         8.686 +- 2.257
     7 L      0.998**       9.081 +- 1.482
     8 P      0.562         5.413 +- 4.116
     9 G      0.805         7.475 +- 3.467
    11 A      0.535         5.191 +- 4.124
    13 S      1.000**       9.097 +- 1.442
    14 S      0.997**       9.071 +- 1.509
    19 V      0.533         5.186 +- 4.141
    20 E      0.999**       9.087 +- 1.467
    27 S      0.943         8.628 +- 2.335



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:   0.998  0.002  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.001  0.008  0.028  0.063  0.114  0.179  0.258  0.349

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 0.001 0.003 0.008
 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 0.046 0.148 0.063
 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 0.047 0.286 0.391 0.005

sum of density on p0-p1 =   1.000000
