
seed used = 139991421

K12                                  GTG TAT TAC CGG TTC GCT ACC AGA GAA GAA TGG GAA GGA AAG GTG AGC ACG AAT CTG ATT TTT AAG GAG TGT CGC CAG AGT GCC GCG ATG AAA CGG GTA TTG AGG GTA TAT AAA AGA ACA TCA 
CFT073                               GTG TAT TAC CGG TTT GCT ACC AAG GAA GAA CGG GAA GGA AAG ATG AGC ACG AAC CTG ATT TTT AAG GAG TGT CGC CAG AGT GCC ACG ATG AAA CGG ATA TTG GCG GTA TAT GGA GTT AAA AGA 
O157                                 GTG TAT TAC CGG TTC GCT ACC AGA GAA GAA CGG GAA GGA AAG GTG AGC ACG AAT CTG ATT TTT AAG GAG TGT CGC CAG AGT GCC GCG ATG AAA CGG GTA TTG AGG GTA TAT AAA AGA ACA TCA 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0542.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 41
# site patterns = 36
    1    2    1    2    1    1    1    1    3    1    1    2    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1

1       
K12                   GTG TAT TAC CGG TTC GCT ACC AGA GAA TGG GGA AAG GTG AGC ACG AAT CTG ATT TTT GAG TGT CGC CAG AGT GCC GCG ATG AAA GTA TTG AGG GTA AAA AGA ACA TCA 
CFT073                ... ... ... ... ..T ... ... .AG ... C.. ... ... A.. ... ... ..C ... ... ... ... ... ... ... ... ... A.. ... ... A.. ... GC. ... GG. GTT .A. AG. 
O157                  ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.21951    C:0.12195    A:0.36585    G:0.29268
position  2:    T:0.24390    C:0.17073    A:0.31707    G:0.26829
position  3:    T:0.19512    C:0.14634    A:0.29268    G:0.36585

#2: CFT073         
position  1:    T:0.17073    C:0.14634    A:0.39024    G:0.29268
position  2:    T:0.26829    C:0.14634    A:0.34146    G:0.24390
position  3:    T:0.21951    C:0.14634    A:0.24390    G:0.39024

#3: O157           
position  1:    T:0.19512    C:0.14634    A:0.36585    G:0.29268
position  2:    T:0.24390    C:0.17073    A:0.31707    G:0.26829
position  3:    T:0.19512    C:0.14634    A:0.29268    G:0.36585

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


Codon position x base (3x4) table, overall

position  1:    T:0.19512    C:0.13821    A:0.37398    G:0.29268
position  2:    T:0.25203    C:0.16260    A:0.32520    G:0.26016
position  3:    T:0.20325    C:0.14634    A:0.27642    G:0.37398

Codon frequencies under model, for use in evolver:
  0.01058048  0.00761794  0.01438945  0.01946808
  0.00682611  0.00491480  0.00928351  0.01256005
  0.01365223  0.00982960  0.00000000  0.00000000
  0.01092178  0.00786368  0.00000000  0.02009608
  0.00749450  0.00539604  0.01019252  0.01378989
  0.00483516  0.00348132  0.00657582  0.00889670
  0.00967033  0.00696264  0.01315164  0.01779340
  0.00773626  0.00557011  0.01052132  0.01423472
  0.02027924  0.01460106  0.02757977  0.03731381
  0.01308338  0.00942004  0.01779340  0.02407343
  0.02616677  0.01884007  0.03558680  0.04814685
  0.02093341  0.01507206  0.02846944  0.03851748
  0.01587071  0.01142691  0.02158417  0.02920211
  0.01023917  0.00737220  0.01392527  0.01884007
  0.02047834  0.01474440  0.02785054  0.03768015
  0.01638267  0.01179552  0.02228043  0.03014412



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                 
CFT073               1.1731 (0.1685 0.1437)
O157                -1.0000 (0.0107 0.0000) 1.1170 (0.1566 0.1402)


TREE #  1:  (1, (2, 3));   MP score: 12
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -225.551013     +0.000000
   4..1     4..5     5..2     5..3  
  0.01108  0.01320  1.07457  0.00000  7.49540  0.09119  0.77848  0.00000 33.49649
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.09886

(1: 0.011084, (2: 1.074567, 3: 0.000004): 0.013201);

(K12: 0.011084, (CFT073: 1.074567, O157: 0.000004): 0.013201);

Detailed output identifying parameters

kappa (ts/tv) =  7.49540


dN/dS for site classes (K=3)

p:   0.09119  0.77848  0.13034
w:   0.00000  1.00000 33.49649

dN & dS for each branch

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

   4..1       0.011     34.7     88.3   5.1443   0.0048   0.0009    0.0    0.4
   4..5       0.013     34.7     88.3   5.1443   0.0057   0.0011    0.0    0.5
   5..2       1.075     34.7     88.3   5.1443   0.4633   0.0901    3.1   40.9
   5..3       0.000     34.7     88.3   5.1443   0.0000   0.0000    0.0    0.0


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

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

    35 R      0.854         28.757
    38 K      0.638         21.733
    39 R      0.994**       33.305
    41 S      0.984*        32.988


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

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

     8 R      0.506         4.458 +- 3.867
    11 W      0.615         5.307 +- 3.872
    29 A      0.510         4.477 +- 3.855
    33 V      0.507         4.453 +- 3.854
    35 R      0.917         7.615 +- 2.782
    38 K      0.874         7.278 +- 3.064
    39 R      0.978*        8.066 +- 2.255
    40 T      0.657         5.638 +- 3.827
    41 S      0.957*        7.916 +- 2.460



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:   0.108  0.109  0.109  0.107  0.104  0.101  0.097  0.093  0.088  0.084
w2:   0.001  0.010  0.026  0.048  0.075  0.105  0.136  0.169  0.200  0.231

Posterior for p0-p1 (see the ternary graph)

 0.001
 0.012 0.003 0.001
 0.019 0.016 0.012 0.003 0.001
 0.015 0.019 0.021 0.017 0.012 0.003 0.001
 0.007 0.013 0.017 0.021 0.022 0.017 0.012 0.003 0.000
 0.003 0.006 0.009 0.014 0.019 0.023 0.023 0.017 0.011 0.002 0.000
 0.001 0.003 0.004 0.007 0.010 0.017 0.021 0.024 0.024 0.016 0.010 0.002 0.000
 0.001 0.001 0.002 0.003 0.005 0.009 0.012 0.019 0.022 0.025 0.024 0.015 0.009 0.002 0.000
 0.000 0.001 0.001 0.002 0.002 0.004 0.006 0.010 0.014 0.020 0.024 0.025 0.023 0.014 0.009 0.002 0.000
 0.000 0.000 0.001 0.001 0.001 0.002 0.003 0.005 0.007 0.012 0.015 0.022 0.024 0.025 0.022 0.013 0.008 0.001 0.000

sum of density on p0-p1 =   1.000000
