
seed used = 139998993

K12                                  ATG CAG ATG CGT CAG CGT GAT GTT GCT GCG CTC GAT GCA AAA TAC ACG AAG GAG TTA GCT GAT GCG AAA GCT GAA AAT GAT GCT CTG CGT GAT GAT GTT GCC GCT GGT CGT CGT CGG TTG CAC ATC AAA GCA GTC TGT --- --- CAG TCA GTG CGT GAA GCC ACC ACC GCC TCC GGC GTG GAT AAT GCA GCC TCC CCC CGA CTG GCA GAC ACC GCT GAA CGG GAT TAT TTC ACC CTC CGG GAA CGA CTG GTA ATG ATG CAG GCC CAA CTT GAA GGT GCT CAG CAA TAC ATA ACC GAG CAG TGT TTA 
CFT073                               ATA CAG ATG CGT CAG CGT GAT GTT GCT GCG CTC GAT GCA AAA TAC ACG AAG GAG TTA GCT GAT GCG AAA GCT GAA AAT GAT GCT CTG CGT GAT GAT GTT GCC GCT GGT CGT CGT CGG TTG CAC ATC AAA GCA GTC TGT --- --- CAG TCA GTG CGT GAA GCC ACC ACC GCC TCC GGC GTG GAT AAT GCA GCC TCC CCC CGA CTG GCA GAC ACC GCT GAA CGG GAT TAT TTC ACC CTC AGA GAG AGG CTG ATC ACT ATG CAA AAA CAA CTG GAA GGA ACC CAG AAG TAT ATT AAT GAG CAG TGC AGA 
O157                                 ATG CAG ATG CGT CAG CGT GAT GTT GCT GCG CTC GAT GCA AAA TAC ACG AAG GAG TTA GCT GAT GCG AAA GCT GAA AAT GAT GCT CTG CAT GAT GAT GTT GCC GCT GGT CGT CGT CGG TTG CAC ATC AAA GCA GTC TGT --- --- CAG TCA GTG CGT GAA GCC ACC ACC GCC TCC GGC GTG GAT AAT GCA GCC TCC CCC CGA CTG GCA GAC ACC GCT GAA CGG GAT TAT TTC ACC CTC AGA GAG AGG CTG ATC ACT ATG CAA AAA CAA CTG GAA GGA ACC CAG AAG TAT ATT AAT GAG CAG TGC AGA 
EDL933                               ATG CAG ATG CGT CAG CGT GAT GTT GCT GCG CTC GAT GCA AAA TAC ACG AAG GAG TTA GCT GAT GCG AAA GCT GAA AAT GAT GCT CTG CAT GAT GAT GTT GCC GCT GGT CGT CGT CGG TTG CAC ATC AAA GCA GTC TGT --- --- CAG TCA GTG CGT GAA GCC ACC ACC GCC TCC GGC GTG GAT AAT GCA GCC TCC CCC CGA CTG GCA GAC ACC GCT GAA CGG GAT TAT TTC ACC CTC AGA GAG AGG CTG ATC ACT ATG CAA AAA CAA CTG GAA GGA ACC CAG AAG TAT ATT AAT GAG CAG TGC AGA 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1362.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 102
# site patterns = 56
    1    5    2    5    8    2    6    2    2    4    3    1    1    1    2
    1    4    2    3    1    4    1    2    1    1    1    1    1    2    1
    2    4    2    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1

K12                                  ATG CAG ATG CGT GAT GTT GCT GCG CTC GCA AAA TAC ACG AAG GAG TTA GAA AAT CTG CGT GCC GGT CGG TTG CAC ATC GTC TGT --- TCA GTG ACC TCC GGC CCC CGA GAC TAT TTC CGG GAA CGA GTA ATG CAG GCC CAA CTT GGT GCT CAA TAC ATA ACC TGT TTA 
CFT073                               ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- ... ... ... ... ... ... ... ... ... ... A.A ..G A.G A.C .CT ..A AAA ... ..G ..A A.C A.G ..T ..T .AT ..C AG. 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... --- ... ... ... ... ... ... ... ... ... ... A.A ..G A.G A.C .CT ..A AAA ... ..G ..A A.C A.G ..T ..T .AT ..C AG. 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... --- ... ... ... ... ... ... ... ... ... ... A.A ..G A.G A.C .CT ..A AAA ... ..G ..A A.C A.G ..T ..T .AT ..C AG. 



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

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

#1: K12            
position  1:    T:0.12000    C:0.27000    A:0.18000    G:0.43000
position  2:    T:0.22000    C:0.28000    A:0.34000    G:0.16000
position  3:    T:0.31000    C:0.23000    A:0.21000    G:0.25000

#2: CFT073         
position  1:    T:0.11000    C:0.24000    A:0.25000    G:0.40000
position  2:    T:0.20000    C:0.27000    A:0.36000    G:0.17000
position  3:    T:0.31000    C:0.23000    A:0.21000    G:0.25000

#3: O157           
position  1:    T:0.11000    C:0.24000    A:0.25000    G:0.40000
position  2:    T:0.20000    C:0.27000    A:0.37000    G:0.16000
position  3:    T:0.31000    C:0.23000    A:0.20000    G:0.26000

#4: EDL933         
position  1:    T:0.11000    C:0.24000    A:0.25000    G:0.40000
position  2:    T:0.20000    C:0.27000    A:0.37000    G:0.16000
position  3:    T:0.31000    C:0.23000    A:0.20000    G:0.26000

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       0 | Ser S TCT       0 | Tyr Y TAT       7 | Cys C TGT       5
      TTC       4 |       TCC       8 |       TAC       5 |       TGC       3
Leu L TTA       5 |       TCA       4 | *** * TAA       0 | *** * TGA       0
      TTG       4 |       TCG       0 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       1 | Pro P CCT       0 | His H CAT       2 | Arg R CGT      22
      CTC       8 |       CCC       4 |       CAC       4 |       CGC       0
      CTA       0 |       CCA       0 | Gln Q CAA       8 |       CGA       5
      CTG      15 |       CCG       0 |       CAG      21 |       CGG       9
------------------------------------------------------------------------------
Ile I ATT       3 | Thr T ACT       3 | Asn N AAT      11 | Ser S AGT       0
      ATC       7 |       ACC      20 |       AAC       0 |       AGC       0
      ATA       2 |       ACA       0 | Lys K AAA      15 | Arg R AGA       6
Met M ATG      12 |       ACG       4 |       AAG       7 |       AGG       3
------------------------------------------------------------------------------
Val V GTT       8 | Ala A GCT      25 | Asp D GAT      32 | Gly G GGT       5
      GTC       4 |       GCC      17 |       GAC       4 |       GGC       4
      GTA       1 |       GCA      16 | Glu E GAA      17 |       GGA       3
      GTG       8 |       GCG       8 |       GAG      11 |       GGG       0
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.11250    C:0.24750    A:0.23250    G:0.40750
position  2:    T:0.20500    C:0.27250    A:0.36000    G:0.16250
position  3:    T:0.31000    C:0.23000    A:0.20500    G:0.25500

Codon frequencies under model, for use in evolver:
  0.00731302  0.00542579  0.00483603  0.00601555
  0.00972097  0.00721233  0.00642838  0.00799628
  0.01284238  0.00952822  0.00000000  0.00000000
  0.00579691  0.00430093  0.00000000  0.00476842
  0.01608865  0.01193674  0.01063927  0.01323421
  0.02138613  0.01586713  0.01414244  0.01759182
  0.02825324  0.02096208  0.01868360  0.02324057
  0.01275320  0.00946205  0.00843357  0.01049053
  0.01511358  0.01121330  0.00999447  0.01243214
  0.02009000  0.01490549  0.01328533  0.01652565
  0.02654092  0.01969165  0.01755126  0.02183205
  0.01198028  0.00888859  0.00792244  0.00985474
  0.02648940  0.01965342  0.01751718  0.02178966
  0.03521151  0.02612467  0.02328503  0.02896431
  0.04651796  0.03451333  0.03076188  0.03826478
  0.02099769  0.01557893  0.01388557  0.01727229



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                 
CFT073               0.2009 (0.0505 0.2515)
O157                 0.1980 (0.0504 0.2543)-1.0000 (0.0089 0.0000)
EDL933               0.1980 (0.0504 0.2543)-1.0000 (0.0089 0.0000)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):   -520.406633     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
 25.67707  0.00000  0.02105  0.00021  0.00000  0.00000  2.24801  0.88941  0.00000  0.00000 998.97330
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  25.69833

(1: 25.677069, (2: 0.021046, (3: 0.000004, 4: 0.000004): 0.000206): 0.000000);

(K12: 25.677069, (CFT073: 0.021046, (O157: 0.000004, EDL933: 0.000004): 0.000206): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.24801


dN/dS for site classes (K=3)

p:   0.88941  0.00000  0.11059
w:   0.00000  1.00000998.97330

dN & dS for each branch

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

   5..1      25.677     86.4    219.6 110.4794  11.8826   0.1076    9.3 2609.8
   5..6       0.000     86.4    219.6 110.4794   0.0000   0.0000    0.0    0.0
   6..2       0.021     86.4    219.6 110.4794   0.0097   0.0001    0.0    2.1
   6..7       0.000     86.4    219.6 110.4794   0.0001   0.0000    0.0    0.0
   7..3       0.000     86.4    219.6 110.4794   0.0000   0.0000    0.0    0.0
   7..4       0.000     86.4    219.6 110.4794   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      1.000**       998.973
    30 R      1.000**       998.973
    80 R      0.749         747.910
    82 R      0.742         740.902
    84 V      1.000**       998.973
    85 M      1.000**       998.973
    88 A      1.000**       998.973
    93 A      1.000**       998.971
    95 Q      1.000**       998.972
    98 T      1.000**       998.972
   102 L      1.000**       998.973


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

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

    30 R      0.845         7.358 +- 3.315
    84 V      0.589         5.294 +- 4.175
    85 M      0.767         6.733 +- 3.716
    88 A      0.972*        8.335 +- 2.281
    95 Q      0.645         5.759 +- 4.105
    98 T      0.549         4.968 +- 4.196
   102 L      0.944         8.141 +- 2.562



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:   0.536  0.265  0.118  0.049  0.019  0.007  0.003  0.001  0.001  0.000
w2:   0.004  0.009  0.019  0.034  0.056  0.085  0.122  0.166  0.220  0.284

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.001
 0.000 0.000 0.000 0.000 0.000 0.001 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.010 0.011
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.010 0.025 0.021
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.007 0.030 0.059 0.033
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.024 0.085 0.114 0.042
 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 0.012 0.071 0.203 0.175 0.039

sum of density on p0-p1 =   1.000000
