
seed used = 139997633

K12                                  ATG GCT CTT CCG CCA GAC CGC ACA GAC AGG GGC GCG GAA CGT TAC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- CTG AAG GAT GAC TGG CAC GGC CTG CAA CTT TTT GCC ATT GAT GGC GCA CAG TTC AGG ACA CCT GAT AAA CCC GAG CTG CGT GAA TAT TAT GGG TCT GCC AAC ACA TCC ACT AAG CGG CAG AAC GCC TAC CCG GTT ATG CGT CTG GTG GCC TTA ATG AAC CTG GGA AGT CAC ATT CTG CTG AAT GCC GTG ACC GCA CCT TAC CGG CAG AGC GAA ACT GTG CTG GCC CAC TCC ATG CTC GCC ACC ATC CCG GAT AAC TCT ATT ACG TTG TTT 
O157                                 TGG CTC TTC CGC CAG ACC ACA CAG ACA TGG GGC GCG GAA CGT TAC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- CTG AAG GAT GAC TGG CAC GGC CTG CAA CTT TTT GCC ATT GAT GGC GCA CAG TTC AGG ACA CCT GAT GAA CCC GAG CTG CGT GAA TAT TAT GGC TCT GCC AAC ACA TCC ACT GAG CGG CAG AGC GCC TAC CCC GTC ATG CGT CTG GTG GCG TTA ATG AAT CTG GGA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATC ACA TTC TAC 
EDL933                               TGG CTC TTC CGC CAG ACC ACA CAG ACA TGG GGC GCG GAA CGT TAC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- CTG AAG GAT GAC TGG CAC GGC CTG CAA CTT TTT GCC ATT GAT GGC GCA CAG TTC AGG ACA CCT GAT GAA CCC GAG CTG CGT GAA TAT TAT GGC TCT GCC AAC ACA TCC ACT GAG CGG CAG AGC GCC TAC CCC GTC ATG CGT CTG GTG GCG TTA ATG AAT CTG GGA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATC ACA TTC TAC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1239.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 120
# site patterns = 81
    1    1    1    1    1    1    1    1    1    1    3    1    2    3    2
   15    5    1    3    1    1    1    1    1    1    3    1    1    2    1
    1    2    1    1    1    1    2    1    1    1    1    1    1    1    1
    1    1    2    1    1    1    1    1    1    2    1    3    1    3    2
    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1

K12                                  ATG GCT CTT CCG CCA GAC CGC ACA GAC AGG GGC GCG GAA CGT TAC --- CTG AAG GAT GAC TGG CAC CAA CTT TTT GCC ATT GCA CAG TTC AGG ACA CCT AAA CCC GAG TAT GGG TCT AAC TCC ACT AAG CGG AAC CCG GTT ATG GTG GCC TTA AAC GGA AGT CAC ATT CTG AAT GCC GTG ACC GCA CCT TAC CGG CAG AGC GAA ACT TCC ATG CTC ATC CCG GAT AAC TCT ATT ACG TTG TTT 
O157                                 TG. CTC T.C .GC .AG AC. ACA CAG ACA T.. ... ... ... ... ... --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ..C ... ... ... ... G.. ... .G. ..C ..C ... ... ..G ... ..T ... --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ..C ..A ..C .AC 
EDL933                               TG. CTC T.C .GC .AG AC. ACA CAG ACA T.. ... ... ... ... ... --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ..C ... ... ... ... G.. ... .G. ..C ..C ... ... ..G ... ..T ... --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ..C ..A ..C .AC 



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

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

#1: K12            
position  1:    T:0.14286    C:0.29524    A:0.26667    G:0.29524
position  2:    T:0.26667    C:0.28571    A:0.29524    G:0.15238
position  3:    T:0.24762    C:0.31429    A:0.12381    G:0.31429

#2: O157           
position  1:    T:0.20270    C:0.28378    A:0.21622    G:0.29730
position  2:    T:0.24324    C:0.24324    A:0.31081    G:0.20270
position  3:    T:0.20270    C:0.33784    A:0.16216    G:0.29730

#3: EDL933         
position  1:    T:0.20270    C:0.28378    A:0.21622    G:0.29730
position  2:    T:0.24324    C:0.24324    A:0.31081    G:0.20270
position  3:    T:0.20270    C:0.33784    A:0.16216    G:0.29730

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       4 | Ser S TCT       4 | Tyr Y TAT       6 | Cys C TGT       0
      TTC       7 |       TCC       4 |       TAC       9 |       TGC       0
Leu L TTA       3 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       1 |       TCG       0 |       TAG       0 | Trp W TGG       7
------------------------------------------------------------------------------
Leu L CTT       4 | Pro P CCT       4 | His H CAT       0 | Arg R CGT       9
      CTC       3 |       CCC       5 |       CAC       5 |       CGC       3
      CTA       0 |       CCA       1 | Gln Q CAA       3 |       CGA       0
      CTG      18 |       CCG       3 |       CAG      11 |       CGG       4
------------------------------------------------------------------------------
Ile I ATT       5 | Thr T ACT       4 | Asn N AAT       3 | Ser S AGT       1
      ATC       3 |       ACC       4 |       AAC       6 |       AGC       3
      ATA       0 |       ACA      13 | Lys K AAA       1 | Arg R AGA       0
Met M ATG       8 |       ACG       1 |       AAG       4 |       AGG       4
------------------------------------------------------------------------------
Val V GTT       1 | Ala A GCT       1 | Asp D GAT      10 | Gly G GGT       0
      GTC       2 |       GCC      13 |       GAC       5 |       GGC      11
      GTA       0 |       GCA       4 | Glu E GAA       9 |       GGA       3
      GTG       5 |       GCG       5 |       GAG       5 |       GGG       1
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.17787    C:0.28854    A:0.23715    G:0.29644
position  2:    T:0.25296    C:0.26087    A:0.30435    G:0.18182
position  3:    T:0.22134    C:0.32806    A:0.14625    G:0.30435

Codon frequencies under model, for use in evolver:
  0.01025780  0.01520352  0.00677747  0.01410447
  0.01057835  0.01567863  0.00698927  0.01454523
  0.01234141  0.01829173  0.00000000  0.00000000
  0.00737279  0.01092753  0.00000000  0.01013759
  0.01664042  0.02466348  0.01099457  0.02288058
  0.01716044  0.02543422  0.01133815  0.02359560
  0.02002051  0.02967325  0.01322784  0.02752820
  0.01196030  0.01772688  0.00790234  0.01644542
  0.01367706  0.02027136  0.00903663  0.01880596
  0.01410447  0.02090484  0.00931902  0.01939364
  0.01645521  0.02438898  0.01087219  0.02262592
  0.00983039  0.01457004  0.00649508  0.01351678
  0.01709633  0.02533920  0.01129579  0.02350745
  0.01763059  0.02613105  0.01164878  0.02424205
  0.02056902  0.03048622  0.01359024  0.02828240
  0.01228798  0.01821255  0.00811885  0.01689598



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                 
O157                 0.4219 (0.1403 0.3325)
EDL933               0.4219 (0.1403 0.3325)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -543.254620     +0.000000
   4..1     4..5     5..2     5..3  
 16.02074 15.88169  0.00000  0.00000  2.46190  0.85631  0.00000  0.22723 598.68078
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  31.90244

(1: 16.020737, (2: 0.000004, 3: 0.000004): 15.881694);

(K12: 16.020737, (O157: 0.000004, EDL933: 0.000004): 15.881694);

Detailed output identifying parameters

kappa (ts/tv) =  2.46190


dN/dS for site classes (K=3)

p:   0.85631  0.00000  0.14369
w:   0.22723  1.00000598.68078

dN & dS for each branch

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

   4..1      16.021     94.9    265.1  86.2170   7.2215   0.0838    7.9 1914.5
   4..5      15.882     94.9    265.1  86.2170   7.1589   0.0830    7.9 1897.9
   5..2       0.000     94.9    265.1  86.2170   0.0000   0.0000    0.0    0.0
   5..3       0.000     94.9    265.1  86.2170   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      0.981*        587.304
     2 A      0.993**       594.426
     3 L      0.640         382.970
     4 P      0.895         535.558
     5 P      0.804         481.311
     6 D      0.930         556.935
     7 R      0.999**       598.244
     8 T      0.998**       597.524
     9 D      0.998**       597.628
   120 F      0.839         502.473


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

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

     1 M      0.915         8.086 +- 2.767
     2 A      0.881         7.814 +- 3.037
     4 P      0.662         6.031 +- 4.080
     5 P      0.570         5.247 +- 4.193
     6 D      0.841         7.483 +- 3.303
     7 R      0.963*        8.471 +- 2.275
     8 T      0.941         8.300 +- 2.517
     9 D      0.956*        8.415 +- 2.352
   120 F      0.528         4.908 +- 4.215



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:   0.320  0.268  0.185  0.110  0.059  0.030  0.015  0.007  0.004  0.002
w2:   0.001  0.004  0.011  0.026  0.048  0.079  0.120  0.171  0.233  0.307

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.001 0.001 0.001
 0.000 0.001 0.002 0.002 0.001
 0.000 0.000 0.000 0.002 0.004 0.004 0.002
 0.000 0.000 0.000 0.000 0.001 0.004 0.011 0.008 0.003
 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.012 0.025 0.013 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.009 0.028 0.047 0.018 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.007 0.022 0.055 0.073 0.020 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.017 0.045 0.087 0.090 0.019 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.009 0.035 0.072 0.109 0.093 0.017 0.002

sum of density on p0-p1 =   1.000000
