
seed used = 140014529

K12                                  GTG GTA GCG GAT CCT ACC ACG ACT CTG CAG GTT AAA AAC ACT GGC AGT CTG AGT GTT AAT CGG TAT GGA TGG ATT AAC ATC TGG ATG GCT ATT TTA GGT CAA TTC TTC ACC CTA TTT CCA CTT TTT TTT GAA TCG TGT CTC ATT CTG TTA AAA ACG TGG CTG GAA ATT TTT CCT GAC AAT GCC GGC ATT CTG CGT ATT TAT CTT TTG CAA TTT TCT GCC ATT GTG GGG TAT AAA ACG CGG CGC GCG GCT 
S2457T                               GTG GTA GCG GAT CCT ACC ACG ACT CTG CAG GTT AAA AAC ACT GGC AGT CTG AGT GTT AAT CGG TAT GGA TGG ATT AAC ATC TGG ATG GCT ATT TTA GGT CAA TTC TTC ACC CGA TTT CCA CTT TTT TTT GAA TCG TGT CTC ATT CTG TTA AAA ACG TGG CTG GAA ATT TTT CCT GAC AAT GCC GGC ATT CTG CGT ATT TAT CTT TTG CAA TTT TCT GCC ATT GTG GGG TAT AAA ACG CGG CGC GCG GCT 
CFT073                               GTG GTA GCG GAT CCT ACC ACG ACT CTG CAG GTT AAA AAC ACT GGC AGT CTG AGT GTT AAT CGG TAT GGA TGG ATT AAC ATC TGG ATG GCT ATT TTA GGT CAG TTC TTC ACC CAA TTT CCA CTT TTT TTT GAA TCG TGT CTC ATT CTG TTA AAA ACG TGG CTG GAA ATT TTT CCT GAC AAT GCT GGC ATT CTG CGT ATT TAT CTT TTG CAA TTT TCT GCC ATT GTG GGG TAT AAA ACG CGG CGC GCG GCT 
O157                                 GTG GTA GCG GAT CCT ACC ACG ACT CTG CAG GTT AAA AAC ACT GGC AGT CTG AGT GTT AAT CGG TAT GGA TGG ATT AAC ATC TGG ATG GCT ATT TTA GGT CAA TTC TTC ACC CGA TTT CCA CTT TTT TTT GAA TCG TGT CTC ATT CTG TTA AAA ACG TGG CTG GAA ATT TTT CCT GAC AAT GCC GGC ATT CTG CGT ATT TAT CTT TTG CAA TTT TCT GCC ATT GTG GGG TAT AAA ACG CGG CGC GCG GCT 
EDL933                               GTG GTA GCG GAT CCT ACC ACG ACT CTG CAG GTT AAA AAC ACT GGC AGT CTG AGT GTT AAT CGG TAT GGA TGG ATT AAC ATC TGG ATG GCT ATT TTA GGT CAA TTC TTC ACC CGA TTT CCA CTT TTT TTT GAA TCG TGT CTC ATT CTG TTA AAA ACG TGG CTG GAA ATT TTT CCT GAC AAT GCC GGC ATT CTG CGT ATT TAT CTT TTG CAA TTT TCT GCC ATT GTG GGG TAT AAA ACG CGG CGC GCG GCT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2941.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 83
# site patterns = 45
    2    1    2    1    2    2    3    2    5    1    2    3    2    2    2
    2    2    3    1    3    7    1    1    2    2    1    1    2    1    5
    1    2    2    1    1    1    1    1    1    1    1    1    1    1    1


1       
K12                   GTG GTA GCG GAT CCT ACC ACG ACT CTG CAG GTT AAA AAC GGC AGT AAT CGG TAT GGA TGG ATT ATC ATG GCT TTA GGT CAA TTC CTA TTT CCA CTT GAA TCG TGT CTC GAC GCC CGT TTG CAA TCT GCC GGG CGC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... .A. ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.22892    C:0.22892    A:0.30120    G:0.24096
position  2:    T:0.39759    C:0.21687    A:0.20482    G:0.18072
position  3:    T:0.40964    C:0.16867    A:0.15663    G:0.26506

#2: S2457T         
position  1:    T:0.22892    C:0.22892    A:0.30120    G:0.24096
position  2:    T:0.38554    C:0.21687    A:0.20482    G:0.19277
position  3:    T:0.40964    C:0.16867    A:0.15663    G:0.26506

#3: CFT073         
position  1:    T:0.22892    C:0.22892    A:0.30120    G:0.24096
position  2:    T:0.38554    C:0.21687    A:0.21687    G:0.18072
position  3:    T:0.42169    C:0.15663    A:0.14458    G:0.27711

#4: O157           
position  1:    T:0.22892    C:0.22892    A:0.30120    G:0.24096
position  2:    T:0.38554    C:0.21687    A:0.20482    G:0.19277
position  3:    T:0.40964    C:0.16867    A:0.15663    G:0.26506

#5: EDL933         
position  1:    T:0.22892    C:0.22892    A:0.30120    G:0.24096
position  2:    T:0.38554    C:0.21687    A:0.20482    G:0.19277
position  3:    T:0.40964    C:0.16867    A:0.15663    G:0.26506

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      25 | Ser S TCT       5 | Tyr Y TAT      15 | Cys C TGT       5
      TTC      10 |       TCC       0 |       TAC       0 |       TGC       0
Leu L TTA      10 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG       5 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT      10 | Pro P CCT      10 | His H CAT       0 | Arg R CGT       5
      CTC       5 |       CCC       0 |       CAC       0 |       CGC       5
      CTA       1 |       CCA       5 | Gln Q CAA      10 |       CGA       3
      CTG      25 |       CCG       0 |       CAG       6 |       CGG      10
------------------------------------------------------------------------------
Ile I ATT      35 | Thr T ACT      10 | Asn N AAT      10 | Ser S AGT      10
      ATC       5 |       ACC      10 |       AAC      10 |       AGC       0
      ATA       0 |       ACA       0 | Lys K AAA      15 | Arg R AGA       0
Met M ATG       5 |       ACG      15 |       AAG       0 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      10 | Ala A GCT      11 | Asp D GAT       5 | Gly G GGT       5
      GTC       0 |       GCC       9 |       GAC       5 |       GGC      10
      GTA       5 |       GCA       0 | Glu E GAA      10 |       GGA       5
      GTG      10 |       GCG      10 |       GAG       0 |       GGG       5
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.22892    C:0.22892    A:0.30120    G:0.24096
position  2:    T:0.38795    C:0.21687    A:0.20723    G:0.18795
position  3:    T:0.41205    C:0.16627    A:0.15422    G:0.26747

Codon frequencies under model, for use in evolver:
  0.03759477  0.01516982  0.01407056  0.02440362
  0.02101571  0.00848002  0.00786553  0.01364178
  0.02008168  0.00810313  0.00000000  0.00000000
  0.01821362  0.00734935  0.00000000  0.01182287
  0.03759477  0.01516982  0.01407056  0.02440362
  0.02101571  0.00848002  0.00786553  0.01364178
  0.02008168  0.00810313  0.00751595  0.01303548
  0.01821362  0.00734935  0.00681679  0.01182287
  0.04946680  0.01996029  0.01851389  0.03211003
  0.02765225  0.01115793  0.01034938  0.01794971
  0.02642326  0.01066202  0.00988941  0.01715194
  0.02396528  0.00967020  0.00896946  0.01555641
  0.03957344  0.01596823  0.01481111  0.02568802
  0.02212180  0.00892634  0.00827950  0.01435976
  0.02113861  0.00852961  0.00791153  0.01372155
  0.01917223  0.00773616  0.00717557  0.01244513



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              -1.0000 (0.0054 0.0000)
CFT073               0.1623 (0.0054 0.0330) 0.1624 (0.0054 0.0330)
O157                -1.0000 (0.0054 0.0000)-1.0000 (0.0000 0.0000) 0.1624 (0.0054 0.0330)
EDL933              -1.0000 (0.0054 0.0000)-1.0000 (0.0000 0.0000) 0.1624 (0.0054 0.0330)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, (4, 5)));   MP score: 4
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):   -351.866727     +0.000000
   6..7     7..1     7..2     6..8     8..3     8..9     9..4     9..5  
  0.00000  0.08412  0.00000  0.00000  0.19328  0.00000  0.00000  0.00000 22.32263  0.98767  0.00000  0.00000 347.95301
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.27741

((1: 0.084116, 2: 0.000004): 0.000000, (3: 0.193284, (4: 0.000004, 5: 0.000004): 0.000000): 0.000000);

((K12: 0.084116, S2457T: 0.000004): 0.000000, (CFT073: 0.193284, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) = 22.32263


dN/dS for site classes (K=3)

p:   0.98767  0.00000  0.01233
w:   0.00000  1.00000347.95301

dN & dS for each branch

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

   6..7       0.000     70.5    178.5   4.2894   0.0000   0.0000    0.0    0.0
   7..1       0.084     70.5    178.5   4.2894   0.0358   0.0084    0.6    6.4
   7..2       0.000     70.5    178.5   4.2894   0.0000   0.0000    0.0    0.0
   6..8       0.000     70.5    178.5   4.2894   0.0000   0.0000    0.0    0.0
   8..3       0.193     70.5    178.5   4.2894   0.0823   0.0192    1.4   14.7
   8..9       0.000     70.5    178.5   4.2894   0.0000   0.0000    0.0    0.0
   9..4       0.000     70.5    178.5   4.2894   0.0000   0.0000    0.0    0.0
   9..5       0.000     70.5    178.5   4.2894   0.0000   0.0000    0.0    0.0


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

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

    38 L      1.000**       347.953


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

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

    38 L      0.804         5.400 +- 3.398



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:   0.258  0.188  0.141  0.107  0.083  0.065  0.052  0.042  0.035  0.029
w2:   0.120  0.097  0.090  0.089  0.090  0.094  0.098  0.102  0.108  0.113

Posterior for p0-p1 (see the ternary graph)

 0.010
 0.004 0.009 0.013
 0.002 0.003 0.005 0.011 0.016
 0.001 0.002 0.002 0.004 0.007 0.014 0.020
 0.001 0.001 0.001 0.002 0.003 0.005 0.008 0.018 0.026
 0.001 0.001 0.001 0.001 0.002 0.002 0.004 0.007 0.011 0.023 0.033
 0.000 0.001 0.001 0.001 0.001 0.002 0.002 0.003 0.005 0.009 0.015 0.031 0.044
 0.000 0.000 0.001 0.001 0.001 0.001 0.001 0.002 0.003 0.004 0.006 0.012 0.020 0.041 0.057
 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.001 0.002 0.003 0.004 0.005 0.008 0.016 0.026 0.055 0.075
 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.001 0.002 0.002 0.003 0.005 0.007 0.011 0.021 0.036 0.074 0.098

sum of density on p0-p1 =   1.000000
