
seed used = 140004137

K12                                  ATG AAC CAT GCA CCG CAT TTA TAT TTC GCC TGG CAA CAA CTC GTC GAA AAA AGC CAG CTC ATG TTA CGC CTG GCA ACG GAA GAA CAA TGG GAC GAA CTC ATC GCC AGC GAA ATG GCG TAT GTG AAT GCG GTG CAG GAG ATT GCA CAT TTG ACT GAA GAG GTT GAC CCG TCC ACC ACG ATG CAG GAG CAG CTC CGC CCG ATG CTG CGC CTG ATT CTC GAC AAC GAA AGC AAG GTA AAG CAG TTA TTA CAG ATT CGG ATG GAT GAA CTG GCG AAA CTG GTC GGT CAG TCA TCG GTG CAA AAA TCG GTG TTA AGT GCC TAT GGC GAT CAG GGC GGC TTT GTG CTG GCT CCG CAG GAT AAC CTC TTT 
S2457T                               ATG AAC AAT GCA CCG CAT TTG TAT TTC GCC TGG CAA CAA CTC GTC GAA AAA AGC CAG CTC ATG TTA CGC CTG GCA ACG GAA GAA CAA TGG GAC GAA CTC ATC GCT AGC GAA ATG GCG TAT GTG AAT GCG GTG CAG GAG ATC GCA CAC CTG ACT GAA GAG GTT GCC CCG TCC ACT ACG ATG CAG GAG CAG CTC CGC CCG ATG CTG CAC CTG ATT CTC GAC AAC GAA AGC AAG GTA AAG CAG TTA TTA CAG ATT CGG ATG GAT GAA CTG GCG AAA CTG GTC GGT CAG TCA TCG GTG CAA AAA TCG GTG TTA AGT GCC TAT GGC GAT CAG GGC GGC TTT GTG CTG GCT CCG CAG GAT AAC CTC TTT 
Shig4337                             ATG AAC AAT GCA CCG CAT TTG TAT TTC GCC TGG CAA CAA CTC GTC GAA AAA AGC CAG CTC ATG TTA CGC CTG GCA ACG GAA GAA CAA TGG GAC GAA CTC ATC GCT AGC GAA ATG GCG TAT GTG AAT GCG GTG CAG GAG ATC GCA CAC CTG ACT GAA GAG GTT GCC CCG TCC ACT ACG ATG CAG GAG CAG CTC CGC CCG ATG CTG CAC CTG ATT CTC GAC AAC GAA AGC AAG GTA AAG CAG TTA TTA CAG ATT CGG ATG GAT GAA CTG GCG AAA CTG GTC GGT CAG TCA TCG GTG CAA AAA TCG GTG TTA AGT GCC TAT GGC GAT CAG GGC GGC TTT GTG CTG GCT CCG CAG GAT AAC CTC TTT 
CFT073                               ATG AAC AAT GCA CCG CAT TTG TAT TTC GCC TGG CAA CAA CTC GTC GAA AAA AGC CAG CTC ATG TTA CGC CTG GCA ACG GAA GAA CAA TGG GAC GAA CTC ATC GCC AGC GAA ATG GCG TAT GTG AAT GCG GTG CAG GAG ATC GCA CAC CTG ACT GAA GAG GTT GCC CCG TCC ACT ACG ATG CAG GAG CAG CTC CGC CCG ATG CTG CAC CTG ATT CTC GAC AAC GAA AGC AAG GTA AAG CAG TTA TTA CAG ATT CGG ATG GAT GAA CTG GCG AAA CTG GTC GGT CAG TCA TCG GTG CAA AAA TCG GTG TTA AGT GCC TAT GGC GAT CAG GGC GGC TTT GTG CTG GCT CCG CAG GAT AAC CTC TTT 
O157                                 ATG AAC CAT GCA CCG CAT TTA TAT TTC GCC TGG CAA CAA CTC GTC GAA AAA AGC CAG CTC ATG TTA CGC CTG GCA ACG GAA GAA CAA TGG GAC GAA CTC ATC GCC AGC GAA ATG GCG TAT GTT AAT GCG GTG CAG GAG ATT GCA CAT TTG ACT GAA GAG GTT GAC CCG TCC ACC ACG ATG CAG GAG CAG CTC CGC CCG ATG CTG CGC CTG ATT CTC GAC AAC GAA AGC AAG GTA AAG CAG TTA TTA CAG ATT CGG ATG GAT GAA CTG GCG AAA CTG GTC GGT CAG TCA TCG GTG CAA AAA TCG GTG TTG AGT GCC TAT GGC GAT CAG GGC GGC TTT GTG CTG GCT CCG CAG GAT AAC CTC TTT 
EDL933                               ATG AAC CAT GCA CCG CAT TTA TAT TTC GCC TGG CAA CAA CTC GTC GAA AAA AGC CAG CTC ATG TTA CGC CTG GCA ACG GAA GAA CAA TGG GAC GAA CTC ATC GCC AGC GAA ATG GCG TAT GTT AAT GCG GTG CAG GAG ATT GCA CAT TTG ACT GAA GAG GTT GAC CCG TCC ACC ACG ATG CAG GAG CAG CTC CGC CCG ATG CTG CGC CTG ATT CTC GAC AAC GAA AGC AAG GTA AAG CAG TTA TTA CAG ATT CGG ATG GAT GAA CTG GCG AAA CTG GTC GGT CAG TCA TCG GTG CAA AAA TCG GTG TTG AGT GCC TAT GGC GAT CAG GGC GGC TTT GTG CTG GCT CCG CAG GAT AAC CTC TTT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1926.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 121
# site patterns = 52
    6    3    1    3    4    1    1    3    1    2    2    4    6    2    8
    3    3    9    3    2    6    2    2    1    1    3    1    1    4    3
    1    1    1    1    1    1    1    1    1    2    2    1    1    3    1
    1    2    1    1    3    2    1

1       
K12                   ATG AAC CAT GCA CCG CAT TTA TAT TTC GCC TGG CAA CTC GTC GAA AAA AGC CAG TTA CGC CTG ACG GAC ATC GCC GCG GTG AAT GTG GAG ATT CAT TTG ACT GTT GAC TCC ACC CGC ATT AAG GTA CGG GAT GGT TCA TCG TTA AGT GGC TTT GCT 
S2457T                ... ... A.. ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ..C ..C C.. ... ... .C. ... ..T .A. ... ... ... ... ... ... ... ... ... ... ... ... ... 
Shig4337              ... ... A.. ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ..C ..C C.. ... ... .C. ... ..T .A. ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... A.. ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..C C.. ... ... .C. ... ..T .A. ... ... ... ... ... ... ... ... ... ... ... ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.14876    C:0.29752    A:0.22314    G:0.33058
position  2:    T:0.33058    C:0.18182    A:0.37190    G:0.11570
position  3:    T:0.16529    C:0.24793    A:0.20661    G:0.38017

#2: S2457T         
position  1:    T:0.14050    C:0.29752    A:0.23140    G:0.33058
position  2:    T:0.33058    C:0.19008    A:0.37190    G:0.10744
position  3:    T:0.16529    C:0.24793    A:0.19835    G:0.38843

#3: Shig4337       
position  1:    T:0.14050    C:0.29752    A:0.23140    G:0.33058
position  2:    T:0.33058    C:0.19008    A:0.37190    G:0.10744
position  3:    T:0.16529    C:0.24793    A:0.19835    G:0.38843

#4: CFT073         
position  1:    T:0.14050    C:0.29752    A:0.23140    G:0.33058
position  2:    T:0.33058    C:0.19008    A:0.37190    G:0.10744
position  3:    T:0.15702    C:0.25620    A:0.19835    G:0.38843

#5: O157           
position  1:    T:0.14876    C:0.29752    A:0.22314    G:0.33058
position  2:    T:0.33058    C:0.18182    A:0.37190    G:0.11570
position  3:    T:0.17355    C:0.24793    A:0.19835    G:0.38017

#6: EDL933         
position  1:    T:0.14876    C:0.29752    A:0.22314    G:0.33058
position  2:    T:0.33058    C:0.18182    A:0.37190    G:0.11570
position  3:    T:0.17355    C:0.24793    A:0.19835    G:0.38017

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      12 | Ser S TCT       0 | Tyr Y TAT      18 | Cys C TGT       0
      TTC       6 |       TCC       6 |       TAC       0 |       TGC       0
Leu L TTA      25 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG       8 |       TCG      12 |       TAG       0 | Trp W TGG      12
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       0 | His H CAT      12 | Arg R CGT       0
      CTC      36 |       CCC       0 |       CAC       6 |       CGC      15
      CTA       0 |       CCA       0 | Gln Q CAA      24 |       CGA       0
      CTG      39 |       CCG      24 |       CAG      54 |       CGG       6
------------------------------------------------------------------------------
Ile I ATT      15 | Thr T ACT       9 | Asn N AAT       9 | Ser S AGT       6
      ATC       9 |       ACC       3 |       AAC      18 |       AGC      18
      ATA       0 |       ACA       0 | Lys K AAA      18 | Arg R AGA       0
Met M ATG      36 |       ACG      12 |       AAG      12 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       8 | Ala A GCT       8 | Asp D GAT      18 | Gly G GGT       6
      GTC      12 |       GCC      19 |       GAC      15 |       GGC      18
      GTA       6 |       GCA      18 | Glu E GAA      48 |       GGA       0
      GTG      28 |       GCG      18 |       GAG      18 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14463    C:0.29752    A:0.22727    G:0.33058
position  2:    T:0.33058    C:0.18595    A:0.37190    G:0.11157
position  3:    T:0.16667    C:0.24931    A:0.19972    G:0.38430

Codon frequencies under model, for use in evolver:
  0.00825439  0.01234747  0.00989162  0.01903284
  0.00464309  0.00694545  0.00556404  0.01070597
  0.00928619  0.01389091  0.00000000  0.00000000
  0.00278586  0.00416727  0.00000000  0.00642358
  0.01698045  0.02540051  0.02034848  0.03915328
  0.00955151  0.01428779  0.01144602  0.02202372
  0.01910301  0.02857558  0.02289204  0.04404744
  0.00573090  0.00857267  0.00686761  0.01321423
  0.01297118  0.01940317  0.01554398  0.02990875
  0.00729629  0.01091428  0.00874349  0.01682367
  0.01459258  0.02182857  0.01748697  0.03364735
  0.00437777  0.00654857  0.00524609  0.01009420
  0.01886717  0.02822279  0.02260942  0.04350364
  0.01061278  0.01587532  0.01271780  0.02447080
  0.02122557  0.03175064  0.02543560  0.04894160
  0.00636767  0.00952519  0.00763068  0.01468248



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               0.1388 (0.0107 0.0773)
Shig4337             0.1388 (0.0107 0.0773)-1.0000 (0.0000 0.0000)
CFT073               0.1681 (0.0107 0.0639) 0.0000 (0.0000 0.0123) 0.0000 (0.0000 0.0123)
O157                 0.0000 (0.0000 0.0250) 0.1022 (0.0107 0.1051) 0.1022 (0.0107 0.1051) 0.1179 (0.0107 0.0911)
EDL933               0.0000 (0.0000 0.0250) 0.1022 (0.0107 0.1051) 0.1022 (0.0107 0.1051) 0.1179 (0.0107 0.0911)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 19
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -567.330340     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.08752  0.00872  0.00000  0.00000  0.00000  0.00000  0.11404  0.00000  0.00000  6.10042  0.97233  0.00000  0.00000 14.96399
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.21031

((1: 0.087524, (2: 0.000004, 3: 0.000004): 0.008718): 0.000000, (4: 0.000004, (5: 0.000004, 6: 0.000004): 0.114043): 0.000000);

((K12: 0.087524, (S2457T: 0.000004, Shig4337: 0.000004): 0.008718): 0.000000, (CFT073: 0.000004, (O157: 0.000004, EDL933: 0.000004): 0.114043): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  6.10042


dN/dS for site classes (K=3)

p:   0.97233  0.00000  0.02767
w:   0.00000  1.00000 14.96399

dN & dS for each branch

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

   7..8       0.000    117.4    245.6   0.4141   0.0000   0.0000    0.0    0.0
   8..1       0.088    117.4    245.6   0.4141   0.0200   0.0483    5.7    4.9
   8..9       0.009    117.4    245.6   0.4141   0.0020   0.0048    0.6    0.5
   9..2       0.000    117.4    245.6   0.4141   0.0000   0.0000    0.0    0.0
   9..3       0.000    117.4    245.6   0.4141   0.0000   0.0000    0.0    0.0
   7..10      0.000    117.4    245.6   0.4141   0.0000   0.0000    0.0    0.0
  10..4       0.000    117.4    245.6   0.4141   0.0000   0.0000    0.0    0.0
  10..11      0.114    117.4    245.6   0.4141   0.0261   0.0630    7.4    6.4
  11..5       0.000    117.4    245.6   0.4141   0.0000   0.0000    0.0    0.0
  11..6       0.000    117.4    245.6   0.4141   0.0000   0.0000    0.0    0.0


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

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

     3 H      1.000**       14.964
    55 D      1.000**       14.964
    69 R      1.000**       14.964


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

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

     3 H      0.936         7.432 +- 2.721
    55 D      0.924         7.345 +- 2.806
    69 R      0.900         7.169 +- 2.953



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:   0.913  0.079  0.008  0.001  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.012  0.022  0.039  0.061  0.087  0.113  0.137  0.159  0.178  0.192

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 0.002 0.015
 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 0.001 0.016 0.108
 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 0.001 0.010 0.131 0.711

sum of density on p0-p1 =   1.000000
