
seed used = 140016653

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3134.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 177
# site patterns = 83
    7    2    5    1    7    2    3    3    1    3   10    5    4    3    2
    2    3    2    1    4    2    1    2    1    6    6    1    4    1    3
    3    1    1    1    1    2    1    2    1    2    3    1    1    1    1
    3    1    1    1    1    1    1    1    1    1    1    2    2    2    3
    2    2    1    1    2    5    3    2    3    1    1    1    1    2    1
    1    1    1    1    1    1    1    1

K12                                  ATG GAA ATC AGC CTG TTG CAG GCA TTT GCG GGC ATT GCC TTT GCT CTG GAT AAC CTA ACC CAT CAC CGC CCG GTG GTC CTC CCG TTG GGG GTA CTT GGA TTA GGT ACG TGG CCT AAC GGT ACT AAA CCC GCA GTA TTC TCG TCC TCT TGC GAC --- CTG GCA ACA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- CGC CGC ATT 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ..G ..C ... ... ..T ... ... ... CGG A.. ..G GAG GCC GAT ACT CGC GGC ATT GAA GTG AAC TAT CTG GCA CTC TTC TTT TGC GCT CCT ATC TAC GCG CAT AAA ACC GTC .AA ..A T.A 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ..G ..C ... ... ..T ... ... ... CGG A.. ..G GAG GCC GAT ACT CGC GGC ATT GAA GTG AAC TAT CTG GCA CTC TTC TTT TGC GCT CCT ATC TAC GCG CAT AAA ACC GTC .AA ..A T.A 
O157                                 ... ... ... ..T ... ... ... ... ..C ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ..A ... ... ... ... ..A ... ... ... ..T ... ... ... ... ... ..T ... ... ... ... ... ..C ... ... ..T ... ... ... CGG A.. ..G GAG GCC GAT ACT CGC GGC ATT GAA GTA AAC TAT CTG GCA CTC TTC TTT TGC GCT CCT ATC TAC GCG CAT AAA ACC GTC .AA ..A T.A 



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

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

#1: K12            
position  1:    T:0.12030    C:0.23308    A:0.24812    G:0.39850
position  2:    T:0.43609    C:0.26316    A:0.12030    G:0.18045
position  3:    T:0.20301    C:0.34586    A:0.12030    G:0.33083

#2: S2457T         
position  1:    T:0.14689    C:0.23164    A:0.23164    G:0.38983
position  2:    T:0.42373    C:0.24859    A:0.16384    G:0.16384
position  3:    T:0.22034    C:0.35028    A:0.12994    G:0.29944

#3: Shig4337       
position  1:    T:0.14689    C:0.23164    A:0.23164    G:0.38983
position  2:    T:0.42373    C:0.24859    A:0.16384    G:0.16384
position  3:    T:0.22034    C:0.35028    A:0.12994    G:0.29944

#4: O157           
position  1:    T:0.14689    C:0.23164    A:0.23164    G:0.38983
position  2:    T:0.42373    C:0.24859    A:0.15819    G:0.16949
position  3:    T:0.23164    C:0.34463    A:0.13559    G:0.28814

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      18 | Ser S TCT       7 | Tyr Y TAT       6 | Cys C TGT       0
      TTC      22 |       TCC       1 |       TAC       3 |       TGC       7
Leu L TTA      11 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG      11 |       TCG       4 |       TAG       0 | Trp W TGG       4
------------------------------------------------------------------------------
Leu L CTT       4 | Pro P CCT      11 | His H CAT      11 | Arg R CGT       0
      CTC      10 |       CCC       4 |       CAC       4 |       CGC      16
      CTA       5 |       CCA       1 | Gln Q CAA       3 |       CGA       3
      CTG      48 |       CCG      19 |       CAG      12 |       CGG       3
------------------------------------------------------------------------------
Ile I ATT      27 | Thr T ACT      18 | Asn N AAT       1 | Ser S AGT       1
      ATC      26 |       ACC      19 |       AAC      14 |       AGC       3
      ATA       0 |       ACA       1 | Lys K AAA       7 | Arg R AGA       0
Met M ATG      31 |       ACG       8 |       AAG       0 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       0 | Ala A GCT      11 | Asp D GAT      20 | Gly G GGT      11
      GTC      30 |       GCC      19 |       GAC       4 |       GGC      49
      GTA      14 |       GCA      24 | Glu E GAA      14 |       GGA       3
      GTG      26 |       GCG      20 |       GAG       3 |       GGG      12
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.14157    C:0.23193    A:0.23494    G:0.39157
position  2:    T:0.42620    C:0.25151    A:0.15361    G:0.16867
position  3:    T:0.21988    C:0.34789    A:0.12952    G:0.30271

Codon frequencies under model, for use in evolver:
  0.01343453  0.02125600  0.00791349  0.01849548
  0.00792780  0.01254329  0.00466980  0.01091429
  0.00484213  0.00766117  0.00000000  0.00000000
  0.00531684  0.00841227  0.00000000  0.00731977
  0.02200976  0.03482366  0.01296465  0.03030110
  0.01298809  0.02054965  0.00765052  0.01788086
  0.00793285  0.01255128  0.00467277  0.01092125
  0.00871058  0.01378180  0.00513089  0.01199196
  0.02229560  0.03527591  0.01313302  0.03069463
  0.01315677  0.02081653  0.00774988  0.01811308
  0.00803587  0.01271429  0.00473346  0.01106308
  0.00882370  0.01396079  0.00519752  0.01214770
  0.03715933  0.05879319  0.02188837  0.05115771
  0.02192794  0.03469421  0.01291646  0.03018847
  0.01339312  0.02119048  0.00788910  0.01843847
  0.01470617  0.02326798  0.00866254  0.02024616



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                 
S2457T               0.2438 (0.0244 0.0999)
Shig4337             0.2438 (0.0244 0.0999)-1.0000 (0.0000 0.0000)
O157                 0.1577 (0.0209 0.1322) 0.0346 (0.0026 0.0744) 0.0346 (0.0026 0.0744)


TREE #  1:  ((1, (2, 3)), 4);   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):   -826.353959     +0.000000
   5..6     6..1     6..7     7..2     7..3     5..4  
  0.04662  0.16927  0.03147  0.00000  0.00000  0.02064  6.46319  0.97070  0.00000  0.01423 19.50084
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.26800

((1: 0.169267, (2: 0.000004, 3: 0.000004): 0.031467): 0.046624, 4: 0.020637);

((K12: 0.169267, (S2457T: 0.000004, Shig4337: 0.000004): 0.031467): 0.046624, O157: 0.020637);

Detailed output identifying parameters

kappa (ts/tv) =  6.46319


dN/dS for site classes (K=3)

p:   0.97070  0.00000  0.02930
w:   0.01423  1.00000 19.50084

dN & dS for each branch

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

   5..6       0.047    168.8    362.2   0.5852   0.0127   0.0217    3.7    4.6
   6..1       0.169    168.8    362.2   0.5852   0.0460   0.0787   13.3   16.7
   6..7       0.031    168.8    362.2   0.5852   0.0086   0.0146    2.5    3.1
   7..2       0.000    168.8    362.2   0.5852   0.0000   0.0000    0.0    0.0
   7..3       0.000    168.8    362.2   0.5852   0.0000   0.0000    0.0    0.0
   5..4       0.021    168.8    362.2   0.5852   0.0056   0.0096    1.6    2.0


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

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

    54 G      0.892         17.401
   127 L      0.591         11.531
   129 T      1.000**       19.499
   175 R      0.997**       19.436
   177 I      0.995**       19.410


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

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

    54 G      0.608         5.258 +- 4.149
   129 T      0.950         7.929 +- 2.564
   175 R      0.914         7.665 +- 2.887
   177 I      0.898         7.556 +- 3.016



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:   0.917  0.078  0.005  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.008  0.014  0.026  0.043  0.067  0.096  0.130  0.167  0.205  0.243

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 0.001
 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 0.011
 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 0.009 0.107
 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 0.005 0.100 0.766

sum of density on p0-p1 =   1.000000
