
seed used = 140004157

K12                                  ATG TCA GCG ATA CAG GGG ATT GAA GGG GTT ATC AGC CAG TTA CAG GCT ACG GCG ATG AGT GCG CGT GCG CAG GAA TCA CTG CCG CAA CCG ACC ATT AGT TTT GCC GGG CAG CTG CAC GCC GCG CTC GAT CGC ATT AGT GAT ACA CAA ACA GCT GCC CGC ACG CAG GCA GAA AAA TTC ACT CTC GGT GAA CCC GGC GTG GCG TTA AAC GAT GTG ATG ACC GAT ATG CAA AAA GCC TCA GTT TCT ATG CAA ATG GGG ATT CAG GTG CGT AAT AAG CTG GTG GCG GCG TAT CAG GAA GTG ATG AGC ATG CAG GTG 
S2457T                               ATG TCA GCG ATA CAG GGG ATT GAA GGG GTT ATC AGC CAG TTA CAG GCT ACG GCG ATG AGT GCG CGT GCG CAG GAA TCA CTG CCG CAA CCG ACC ATT AGT TTT GCC GGG CAG CTG CAC GCC GCG CTC GAT CGC ATA AGC GAT ACA CAA ACA GTC GCC CGC ACG CAG GCA GAA AAA TTC ACC CTC GGT GAA CCC GGC GTG GCG CTA AAC GAT GTG ATG ACC GAT ATG CAA AAA GCC TCA GTT TCT ATG CAA ATG GGG ATT CAG GTG CGT AAT AAG CTG GTG GCG GCG TAT CAG GAA GTG ATG TCC ATG CAG GTG 
Shig4337                             ATG TCA GCG ATA CAG GGG ATT GAA GGG GTT ATC AGC CAG TTA CAG GCT ACG GCG ATG AGT GCG CGT GCG CAG GAA TCA CTG CCG CAA CCG ACC ATT AGT TTT GCC GGG CAG CTG CAC GCC GCG CTC GAT CGC ATA AGC GAT ACA CAA ACA GTC GCC CGC ACG CAG GCA GAA AAA TTC ACC CTC GGT GAA CCC GGC GTG GCG CTA AAC GAT GTG ATG ACC GAT ATG CAA AAA GCC TCA GTT TCT ATG CAA ATG GGG ATT CAG GTG CGT AAT AAG CTG GTG GCG GCG TAT CAG GAA GTG ATG TCC ATG CAG GTG 
CFT073                               ATG TCA GCG ATA CAG GGG ATT GAA GGG GTT ATC AGC CAG TTA CAG GCT ACG GCG ATG AGT GCG CGT GCG CAG GAA TCA CTG CCG CAA CCG ACC ATT AGT TTT GCC GGG CAG CTG CAC GCC GCG CTC GAT CGC ATA AGC GAT ACA CAA ACA GTC GCC CGC ACG CAG GCA GAA AAA TTC ACC CTC GGT GAA CCC GGC GTG GCG CTA AAC GAT GTG ATG ACC GAT ATG CAA AAA GCC TCA GTT TCT ATG CAA ATG GGG ATT CAG GTG CGT AAT AAG CTG GTG GCG GCG TAT CAG GAA GTG ATG TCC ATG CAG GTG 
O157                                 ATG TCA GCG ATA CAG GGG ATT GAA GGG GTT ATC AGC CAG TTA CAG GCT ACG GCG ATG AGT GCG CGT GCG CAG GAA TCA CTG CCG CAA CCG ACC ATT AGT TTT GCC GGG CAG CTG CAC GCC GCG CTC GAT CGC ATA AGC GAT ACA CAA ACA GCC GCC CGC ACG CAG GCA GAA AAA TTC ACT CTC GGT GAA CCC GGC GTG GCG TTA AAC GAT GTG ATG ACC GAT ATG CAA AAA GCC TCA GTT TCT ATG CAA ATG GGG ATT CAG GTG CGT AAT AAG CTG GTG GCG GCA TAT CAG GAA GTA ATG AGC ATG CAG GTA 
EDL933                               ATG TCA GCG ATA CAG GGG ATT GAA GGG GTT ATC AGC CAG TTA CAG GCT ACG GCG ATG AGT GCG CGT GCG CAG GAA TCA CTG CCG CAA CCG ACC ATT AGT TTT GCC GGG CAG CTG CAC GCC GCG CTC GAT CGC ATA AGC GAT ACA CAA ACA GCC GCC CGC ACG CAG GCA GAA AAA TTC ACT CTC GGT GAA CCC GGC GTG GCG TTA AAC GAT GTG ATG ACC GAT ATG CAA AAA GCC TCA GTT TCT ATG CAA ATG GGG ATT CAG GTG CGT AAT AAG CTG GTG GCG GCA TAT CAG GAA GTA ATG AGC ATG CAG GTA 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1937.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 104
# site patterns = 47
    8    3    7    1    9    4    3    5    2    1    1    1    1    2    2
    2    3    2    4    2    1    4    1    2    4    2    1    1    2    1
    1    2    1    1    1    1    1    4    1    1    1    1    1    1    1
    2    1

1       
K12                   ATG TCA GCG ATA CAG GGG ATT GAA GTT ATC AGC TTA GCT ACG AGT CGT CTG CCG CAA ACC TTT GCC CAC CTC GAT CGC ATT AGT ACA GCT GCA AAA TTC ACT GGT CCC GGC GTG TTA AAC TCT AAT AAG GCG TAT GTG AGC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..C ... .TC ... ... ... ..C ... ... ... ... C.. ... ... ... ... ... ... ... TC. 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..C ... .TC ... ... ... ..C ... ... ... ... C.. ... ... ... ... ... ... ... TC. 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..C ... .TC ... ... ... ..C ... ... ... ... C.. ... ... ... ... ... ... ... TC. 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..C ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ..A ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..C ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ..A ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  1  1  1  1  1  1 | Ser TCT  1  1  1  1  1  1 | Tyr TAT  1  1  1  1  1  1 | Cys TGT  0  0  0  0  0  0
    TTC  1  1  1  1  1  1 |     TCC  0  1  1  1  0  0 |     TAC  0  0  0  0  0  0 |     TGC  0  0  0  0  0  0
Leu TTA  2  1  1  1  2  2 |     TCA  3  3  3  3  3  3 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  0  0  0  0  0  0 |     TCG  0  0  0  0  0  0 |     TAG  0  0  0  0  0  0 | Trp TGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Leu CTT  0  0  0  0  0  0 | Pro CCT  0  0  0  0  0  0 | His CAT  0  0  0  0  0  0 | Arg CGT  2  2  2  2  2  2
    CTC  2  2  2  2  2  2 |     CCC  1  1  1  1  1  1 |     CAC  1  1  1  1  1  1 |     CGC  2  2  2  2  2  2
    CTA  0  1  1  1  0  0 |     CCA  0  0  0  0  0  0 | Gln CAA  4  4  4  4  4  4 |     CGA  0  0  0  0  0  0
    CTG  3  3  3  3  3  3 |     CCG  2  2  2  2  2  2 |     CAG  9  9  9  9  9  9 |     CGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT  4  3  3  3  3  3 | Thr ACT  1  0  0  0  1  1 | Asn AAT  1  1  1  1  1  1 | Ser AGT  3  2  2  2  2  2
    ATC  1  1  1  1  1  1 |     ACC  2  3  3  3  2  2 |     AAC  1  1  1  1  1  1 |     AGC  2  2  2  2  3  3
    ATA  1  2  2  2  2  2 |     ACA  2  2  2  2  2  2 | Lys AAA  2  2  2  2  2  2 | Arg AGA  0  0  0  0  0  0
Met ATG  8  8  8  8  8  8 |     ACG  2  2  2  2  2  2 |     AAG  1  1  1  1  1  1 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  2  2  2  2  2  2 | Ala GCT  2  1  1  1  1  1 | Asp GAT  4  4  4  4  4  4 | Gly GGT  1  1  1  1  1  1
    GTC  0  1  1  1  0  0 |     GCC  4  4  4  4  5  5 |     GAC  0  0  0  0  0  0 |     GGC  1  1  1  1  1  1
    GTA  0  0  0  0  2  2 |     GCA  1  1  1  1  2  2 | Glu GAA  5  5  5  5  5  5 |     GGA  0  0  0  0  0  0
    GTG  6  6  6  6  4  4 |     GCG  8  8  8  8  7  7 |     GAG  0  0  0  0  0  0 |     GGG  4  4  4  4  4  4
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.08654    C:0.25000    A:0.29808    G:0.36538
position  2:    T:0.29808    C:0.27885    A:0.27885    G:0.14423
position  3:    T:0.22115    C:0.17308    A:0.19231    G:0.41346

#2: S2457T         
position  1:    T:0.08654    C:0.25962    A:0.28846    G:0.36538
position  2:    T:0.30769    C:0.27885    A:0.27885    G:0.13462
position  3:    T:0.18269    C:0.20192    A:0.20192    G:0.41346

#3: Shig4337       
position  1:    T:0.08654    C:0.25962    A:0.28846    G:0.36538
position  2:    T:0.30769    C:0.27885    A:0.27885    G:0.13462
position  3:    T:0.18269    C:0.20192    A:0.20192    G:0.41346

#4: CFT073         
position  1:    T:0.08654    C:0.25962    A:0.28846    G:0.36538
position  2:    T:0.30769    C:0.27885    A:0.27885    G:0.13462
position  3:    T:0.18269    C:0.20192    A:0.20192    G:0.41346

#5: O157           
position  1:    T:0.08654    C:0.25000    A:0.29808    G:0.36538
position  2:    T:0.29808    C:0.27885    A:0.27885    G:0.14423
position  3:    T:0.19231    C:0.19231    A:0.23077    G:0.38462

#6: EDL933         
position  1:    T:0.08654    C:0.25000    A:0.29808    G:0.36538
position  2:    T:0.29808    C:0.27885    A:0.27885    G:0.14423
position  3:    T:0.19231    C:0.19231    A:0.23077    G:0.38462

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       6 | Ser S TCT       6 | Tyr Y TAT       6 | Cys C TGT       0
      TTC       6 |       TCC       3 |       TAC       0 |       TGC       0
Leu L TTA       9 |       TCA      18 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       0 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       0 | His H CAT       0 | Arg R CGT      12
      CTC      12 |       CCC       6 |       CAC       6 |       CGC      12
      CTA       3 |       CCA       0 | Gln Q CAA      24 |       CGA       0
      CTG      18 |       CCG      12 |       CAG      54 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      19 | Thr T ACT       3 | Asn N AAT       6 | Ser S AGT      13
      ATC       6 |       ACC      15 |       AAC       6 |       AGC      14
      ATA      11 |       ACA      12 | Lys K AAA      12 | Arg R AGA       0
Met M ATG      48 |       ACG      12 |       AAG       6 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      12 | Ala A GCT       7 | Asp D GAT      24 | Gly G GGT       6
      GTC       3 |       GCC      26 |       GAC       0 |       GGC       6
      GTA       4 |       GCA       8 | Glu E GAA      30 |       GGA       0
      GTG      32 |       GCG      46 |       GAG       0 |       GGG      24
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.08654    C:0.25481    A:0.29327    G:0.36538
position  2:    T:0.30288    C:0.27885    A:0.27885    G:0.13942
position  3:    T:0.19231    C:0.19391    A:0.20994    G:0.40385

Codon frequencies under model, for use in evolver:
  0.00512958  0.00517232  0.00559979  0.01077211
  0.00472247  0.00476182  0.00515536  0.00991718
  0.00472247  0.00476182  0.00000000  0.00000000
  0.00236123  0.00238091  0.00000000  0.00495859
  0.01510376  0.01522962  0.01648827  0.03171789
  0.01390504  0.01402092  0.01517967  0.02920059
  0.01390504  0.01402092  0.01517967  0.02920059
  0.00695252  0.00701046  0.00758984  0.01460030
  0.01738357  0.01752843  0.01897706  0.03650549
  0.01600392  0.01613729  0.01747095  0.03360823
  0.01600392  0.01613729  0.01747095  0.03360823
  0.00800196  0.00806864  0.00873547  0.01680412
  0.02165822  0.02183870  0.02364355  0.04548225
  0.01993931  0.02010547  0.02176708  0.04187255
  0.01993931  0.02010547  0.02176708  0.04187255
  0.00996965  0.01005273  0.01088354  0.02093627



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               0.1779 (0.0127 0.0713)
Shig4337             0.1779 (0.0127 0.0713)-1.0000 (0.0000 0.0000)
CFT073               0.1779 (0.0127 0.0713)-1.0000 (0.0000 0.0000)-1.0000 (0.0000 0.0000)
O157                 0.0000 (0.0000 0.0872) 0.1779 (0.0127 0.0713) 0.1779 (0.0127 0.0713) 0.1779 (0.0127 0.0713)
EDL933               0.0000 (0.0000 0.0872) 0.1779 (0.0127 0.0713) 0.1779 (0.0127 0.0713) 0.1779 (0.0127 0.0713)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 13
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -477.834084     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.43770  0.00000  0.00000  0.00000  0.00000  0.00000  0.38930  0.00000  0.00000  9.22702  0.98018  0.00000  0.00000 150.38663
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.82702

((1: 0.437705, (2: 0.000004, 3: 0.000004): 0.000000): 0.000000, (4: 0.000004, (5: 0.000004, 6: 0.000004): 0.389296): 0.000000);

((K12: 0.437705, (S2457T: 0.000004, Shig4337: 0.000004): 0.000000): 0.000000, (CFT073: 0.000004, (O157: 0.000004, EDL933: 0.000004): 0.389296): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  9.22702


dN/dS for site classes (K=3)

p:   0.98018  0.00000  0.01982
w:   0.00000  1.00000150.38663

dN & dS for each branch

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

   7..8       0.000     93.9    218.1   2.9812   0.0000   0.0000    0.0    0.0
   8..1       0.438     93.9    218.1   2.9812   0.1824   0.0612    5.7   39.8
   8..9       0.000     93.9    218.1   2.9812   0.0000   0.0000    0.0    0.0
   9..2       0.000     93.9    218.1   2.9812   0.0000   0.0000    0.0    0.0
   9..3       0.000     93.9    218.1   2.9812   0.0000   0.0000    0.0    0.0
   7..10      0.000     93.9    218.1   2.9812   0.0000   0.0000    0.0    0.0
  10..4       0.000     93.9    218.1   2.9812   0.0000   0.0000    0.0    0.0
  10..11      0.389     93.9    218.1   2.9812   0.1622   0.0544    5.1   35.4
  11..5       0.000     93.9    218.1   2.9812   0.0000   0.0000    0.0    0.0
  11..6       0.000     93.9    218.1   2.9812   0.0000   0.0000    0.0    0.0


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

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

    51 A      1.000**       150.387
   101 S      1.000**       150.387


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

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

    51 A      0.923         8.364 +- 2.653
   101 S      0.999**       8.960 +- 1.645



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:   0.906  0.085  0.008  0.001  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.002  0.007  0.018  0.036  0.066  0.109  0.169  0.247  0.345

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 0.002
 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 0.014
 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 0.012 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 0.000 0.004 0.100 0.760

sum of density on p0-p1 =   1.000000
