
seed used = 140004333

K12                                  ATG AGT GAC ATG AAT AAT CCG GCC GAT GAC AAC AAC GGC GCA ATG GAC GAT CTG TGG GCT GAA GCG TTG AGC GAA CAA AAA TCA ACC AGC AGC AAA AGC GCT GCC GAG ACG GTG TTC CAG CAA TTT GGC GGT GGT GAT GTC AGC GGA ACG TTG CAG GAT ATC GAC CTG ATT ATG GAT ATT CCG GTC AAG CTG ACC GTC GAG CTG GGC CGT ACG CGG ATG ACC ATC AAA GAG CTG TTG CGT CTG ACG CAA GGG TCC GTC GTG GCG CTG GAC GGT CTG GCG GGC GAA CCA CTG GAT ATT CTG ATC AAC GGT TAT TTA ATC GCC CAG GGC GAA GTG GTG GTC GTT GCC GAT AAA TAT GGC GTG CGG ATC ACC GAT ATC ATT ACT CCG TCT GAG CGA ATG CGC CGC CTG AGC CGT 
S2457T                               ATG AGT GAC ATG AAT AAT CCG GCC GAT GAC AAC AAC GGC GCA ATG GAC GAT CTG TGG GCT GAA GCG TTG AGC GAG CAA AAA TCA ACC AGC GAA AAA AGC GCT GCC GAC GCG GTG TTC CAG CAA TTT GGC GGT GGT GAT GTC AGC GGA ACG TTG CAG GAT ATC GAC CTG ATT ATG GAT ATT CCG GTC AAG CTG ACC GTC GAG CTG GGC CGT ACG CGG ATG ACC ATC AAA GAG CTG TTG CGT CTG ACG CAA GGG TCA GTC GTG GCG CTG GAC GGT CTG GCG GGC GAA CCG CTG GAT ATT CTG ATC AAC GGT TAT TTA ATC GCC CAG GGC GAA GTG GTG GTT GTT GCC GAT AAA TAT GGC GTG CGG ATC ACC GAT ATC ATT ACC CCG TCC GAG CGG ATG CGC CGC CTG AGC CGT 
Shig4337                             ATG AGT GAC ATG AAT AAT CCG GCC GAT GAC AAC AAC GGC GCA ATG GAC GAT CTG TGG GCT GAA GCG TTG AGC GAG CAA AAA TCA ACC AGC GAA AAA AGC GCT GCC GAC GCG GTG TTC CAG CAA TTT GGC GGT GGT GAT GTC AGC GGA ACG TTG CAG GAT ATC GAC CTG ATT ATG GAT ATT CCG GTC AAG CTG ACC GTC GAG CTG GGC CGT ACG CGG ATG ACC ATC AAA GAG CTG TTG CGT CTG ACG CAA GGG TCA GTC GTG GCG CTG GAC GGT CTG GCG GGC GAA CCG CTG GAT ATT CTG ATC AAC GGT TAT TTA ATC GCC CAG GGC GAA GTG GTG GTT GTT GCC GAT AAA TAT GGC GTG CGG ATC ACC GAT ATC ATT ACC CCG TCC GAG CGG ATG CGC CGC CTG AGC CGT 
CFT073                               ATG AGT GAC ATG AAT AAT CCG GCC GAT GAC AAC AAC GGC GCA ATG GAC GAT CTG TGG GCT GAA GCG TTG AGC GAG CAA AAA TCA ACC AGC GGA AAA AGC GCT ACC GAT GCG GTG TTC CAG CAA TTT GGC GGT GGT GAT GTC AGC GGA ACG TTG CAG GAT ATC GAC CTG ATT ATG GAT ATT CCG GTC AAG CTG ACC GTC GAG CTG GGC CGT ACG CGG ATG ACC ATC AAA GAG CTG TTG CGT CTG ACG CAA GGG TCC GTC GTG GCG CTG GAC GGT CTG GCG GGC GAA CCG CTG GAT ATT CTG ATC AAC GGT TAT TTA ATC GCC CAG GGC GAA GTG GTG GTT GTT GCC GAT AAA TAT GGC GTG CGG ATC ACC GAT ATC ATT ACC CCG TCC GAG CGG ATG CGC CGC CTG AGC CGT 
O157                                 ATG AGT GAC ATG AAT AAT CCG GCC GAT GAC AAC AAC GGC GCA ATG GAC GAT CTG TGG GCT GAA GCG TTG AGC GAA CAA AAA TCA ACC AGC AGC AAA AGC GCT GCC GAC GCG GTG TTC CAG CAA TTT GGC GGT GGT GAT GTC AGC GGA ACG TTG CAG GAT ATC GAC CTG ATT ATG GAT ATT CCG GTC AAG CTG ACC GTC GAG CTG GGC CGC ACA CGA ATG ACC ATC AAA GAG CTG TTG CGT CTG ACG CAA GGG TCC GTC GTG GCG CTG GAC GGT CTG GCG GGC GAA CCA CTG GAT ATT CTG ATC AAC GGT TAT TTA ATC GCC CAG GGC GAA GTG GTG GTC GTT GCC GAT AAA TAT GGC GTG CGG ATC ACC GAT ATC ATT ACT CCG TCT GAG CGA ATG CGC CGC CTG AGC CGT 
EDL933                               ATG AGT GAC ATG AAT AAT CCG GCC GAT GAC AAC AAC GGC GCA ATG GAC GAT CTG TGG GCT GAA GCG TTG AGC GAA CAA AAA TCA ACC AGC AGC AAA AGC GCT GCC GAC GCG GTG TTC CAG CAA TTT GGC GGT GGT GAT GTC AGC GGA ACG TTG CAG GAT ATC GAC CTG ATT ATG GAT ATT CCG GTC AAG CTG ACC GTC GAG CTG GGC CGC ACA CGA ATG ACC ATC AAA GAG CTG TTG CGT CTG ACG CAA GGG TCC GTC GTG GCG CTG GAC GGT CTG GCG GGC GAA CCA CTG GAT ATT CTG ATC AAC GGT TAT TTA ATC GCC CAG GGC GAA GTG GTG GTC GTT GCC GAT AAA TAT GGC GTG CGG ATC ACC GAT ATC ATT ACT CCG TCT GAG CGA ATG CGC CGC CTG AGC CGT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1946.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 137
# site patterns = 54
    6    1    5    2    3    3    8    3    6    1   11    1    2    3    3
    3    5    1    3    4    1    4    1    1    1    1    5    1    3    1
    4    4    1    2    6    4    1    3    1    1    1    2    1    1    1
    2    1    1    1    1    1    1    1    2

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  1  1  1  1  1  1 | Ser TCT  1  0  0  0  1  1 | Tyr TAT  2  2  2  2  2  2 | Cys TGT  0  0  0  0  0  0
    TTC  1  1  1  1  1  1 |     TCC  1  1  1  2  1  1 |     TAC  0  0  0  0  0  0 |     TGC  0  0  0  0  0  0
Leu TTA  1  1  1  1  1  1 |     TCA  1  2  2  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  3  3  3  3  3  3 |     TCG  0  0  0  0  0  0 |     TAG  0  0  0  0  0  0 | Trp TGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------
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  3  3  3  3  2  2
    CTC  0  0  0  0  0  0 |     CCC  0  0  0  0  0  0 |     CAC  0  0  0  0  0  0 |     CGC  2  2  2  2  3  3
    CTA  0  0  0  0  0  0 |     CCA  1  0  0  0  1  1 | Gln CAA  3  3  3  3  3  3 |     CGA  1  0  0  0  2  2
    CTG 11 11 11 11 11 11 |     CCG  3  4  4  4  3  3 |     CAG  3  3  3  3  3  3 |     CGG  2  3  3  3  1  1
--------------------------------------------------------------------------------------------------------------
Ile ATT  4  4  4  4  4  4 | Thr ACT  1  0  0  0  1  1 | Asn AAT  2  2  2  2  2  2 | Ser AGT  1  1  1  1  1  1
    ATC  6  6  6  6  6  6 |     ACC  4  5  5  6  4  4 |     AAC  3  3  3  3  3  3 |     AGC  6  5  5  5  6  6
    ATA  0  0  0  0  0  0 |     ACA  0  0  0  0  1  1 | Lys AAA  4  4  4  4  4  4 | Arg AGA  0  0  0  0  0  0
Met ATG  6  6  6  6  6  6 |     ACG  4  3  3  3  2  2 |     AAG  1  1  1  1  1  1 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  1  2  2  2  1  1 | Ala GCT  2  2  2  2  2  2 | Asp GAT  8  8  8  9  8  8 | Gly GGT  4  4  4  4  4  4
    GTC  5  4  4  4  5  5 |     GCC  4  4  4  3  4  4 |     GAC  5  6  6  5  6  6 |     GGC  6  6  6  6  6  6
    GTA  0  0  0  0  0  0 |     GCA  1  1  1  1  1  1 | Glu GAA  4  4  4  3  4  4 |     GGA  1  1  1  2  1  1
    GTG  5  5  5  5  5  5 |     GCG  3  4  4  4  4  4 |     GAG  4  4  4  4  3  3 |     GGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.08759    C:0.21168    A:0.30657    G:0.39416
position  2:    T:0.32117    C:0.18978    A:0.28467    G:0.20438
position  3:    T:0.21898    C:0.31387    A:0.12409    G:0.34307

#2: S2457T         
position  1:    T:0.08759    C:0.21168    A:0.29197    G:0.40876
position  2:    T:0.32117    C:0.18978    A:0.29197    G:0.19708
position  3:    T:0.21168    C:0.31387    A:0.11679    G:0.35766

#3: Shig4337       
position  1:    T:0.08759    C:0.21168    A:0.29197    G:0.40876
position  2:    T:0.32117    C:0.18978    A:0.29197    G:0.19708
position  3:    T:0.21168    C:0.31387    A:0.11679    G:0.35766

#4: CFT073         
position  1:    T:0.08759    C:0.21168    A:0.29927    G:0.40146
position  2:    T:0.32117    C:0.18978    A:0.28467    G:0.20438
position  3:    T:0.21898    C:0.31387    A:0.10949    G:0.35766

#5: O157           
position  1:    T:0.08759    C:0.21168    A:0.29927    G:0.40146
position  2:    T:0.32117    C:0.18978    A:0.28467    G:0.20438
position  3:    T:0.21168    C:0.32847    A:0.13869    G:0.32117

#6: EDL933         
position  1:    T:0.08759    C:0.21168    A:0.29927    G:0.40146
position  2:    T:0.32117    C:0.18978    A:0.28467    G:0.20438
position  3:    T:0.21168    C:0.32847    A:0.13869    G:0.32117

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       6 | Ser S TCT       3 | Tyr Y TAT      12 | Cys C TGT       0
      TTC       6 |       TCC       7 |       TAC       0 |       TGC       0
Leu L TTA       6 |       TCA       8 | *** * TAA       0 | *** * TGA       0
      TTG      18 |       TCG       0 |       TAG       0 | Trp W TGG       6
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       0 | His H CAT       0 | Arg R CGT      16
      CTC       0 |       CCC       0 |       CAC       0 |       CGC      14
      CTA       0 |       CCA       3 | Gln Q CAA      18 |       CGA       5
      CTG      66 |       CCG      21 |       CAG      18 |       CGG      13
------------------------------------------------------------------------------
Ile I ATT      24 | Thr T ACT       3 | Asn N AAT      12 | Ser S AGT       6
      ATC      36 |       ACC      28 |       AAC      18 |       AGC      33
      ATA       0 |       ACA       2 | Lys K AAA      24 | Arg R AGA       0
Met M ATG      36 |       ACG      17 |       AAG       6 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       9 | Ala A GCT      12 | Asp D GAT      49 | Gly G GGT      24
      GTC      27 |       GCC      23 |       GAC      34 |       GGC      36
      GTA       0 |       GCA       6 | Glu E GAA      23 |       GGA       7
      GTG      30 |       GCG      23 |       GAG      22 |       GGG       6
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.08759    C:0.21168    A:0.29805    G:0.40268
position  2:    T:0.32117    C:0.18978    A:0.28710    G:0.20195
position  3:    T:0.21411    C:0.31873    A:0.12409    G:0.34307

Codon frequencies under model, for use in evolver:
  0.00610846  0.00909327  0.00354013  0.00978741
  0.00360954  0.00537330  0.00209189  0.00578347
  0.00546059  0.00812883  0.00000000  0.00000000
  0.00384092  0.00571774  0.00000000  0.00615421
  0.01476211  0.02197541  0.00855531  0.02365292
  0.00872306  0.01298547  0.00505541  0.01397672
  0.01319643  0.01964468  0.00764793  0.02114428
  0.00928223  0.01381787  0.00537948  0.01487267
  0.02078572  0.03094238  0.01204627  0.03330440
  0.01228247  0.01828414  0.00711825  0.01967987
  0.01858118  0.02766062  0.01076864  0.02977211
  0.01306981  0.01945620  0.00757455  0.02094140
  0.02808194  0.04180379  0.01627476  0.04499492
  0.01659387  0.02470224  0.00961690  0.02658791
  0.02510355  0.03737006  0.01454865  0.04022273
  0.01765758  0.02628572  0.01023337  0.02829226



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               0.2109 (0.0157 0.0747)
Shig4337             0.2109 (0.0157 0.0747)-1.0000 (0.0000 0.0000)
CFT073               0.2181 (0.0147 0.0672) 0.3234 (0.0065 0.0200) 0.3234 (0.0065 0.0200)
O157                 0.2132 (0.0065 0.0304) 0.0849 (0.0092 0.1083) 0.0849 (0.0092 0.1083) 0.0725 (0.0081 0.1118)
EDL933               0.2132 (0.0065 0.0304) 0.0849 (0.0092 0.1083) 0.0849 (0.0092 0.1083) 0.0725 (0.0081 0.1118)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 22
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -661.913574     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.04034  0.08906  0.00000  0.00000  0.00000  0.10491  0.05328  0.00000  0.00000 12.20048  0.99246  0.00000  0.07210 59.48425
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.28760

((1: 0.040336, (2: 0.000004, 3: 0.000004): 0.089060): 0.000000, (4: 0.104907, (5: 0.000004, 6: 0.000004): 0.053280): 0.000000);

((K12: 0.040336, (S2457T: 0.000004, Shig4337: 0.000004): 0.089060): 0.000000, (CFT073: 0.104907, (O157: 0.000004, EDL933: 0.000004): 0.053280): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) = 12.20048


dN/dS for site classes (K=3)

p:   0.99246  0.00000  0.00754
w:   0.07210  1.00000 59.48425

dN & dS for each branch

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

   7..8       0.000    117.7    293.3   0.5204   0.0000   0.0000    0.0    0.0
   8..1       0.040    117.7    293.3   0.5204   0.0106   0.0204    2.4    3.1
   8..9       0.089    117.7    293.3   0.5204   0.0235   0.0451    5.3    6.9
   9..2       0.000    117.7    293.3   0.5204   0.0000   0.0000    0.0    0.0
   9..3       0.000    117.7    293.3   0.5204   0.0000   0.0000    0.0    0.0
   7..10      0.000    117.7    293.3   0.5204   0.0000   0.0000    0.0    0.0
  10..4       0.105    117.7    293.3   0.5204   0.0277   0.0532    6.3    8.1
  10..11      0.053    117.7    293.3   0.5204   0.0141   0.0270    3.2    4.1
  11..5       0.000    117.7    293.3   0.5204   0.0000   0.0000    0.0    0.0
  11..6       0.000    117.7    293.3   0.5204   0.0000   0.0000    0.0    0.0


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

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

    31 S      1.000**       59.484


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

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

    31 S      0.995**       7.778 +- 2.334



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:   0.861  0.130  0.009  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.011  0.025  0.043  0.064  0.085  0.107  0.130  0.153  0.178  0.204

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 0.001
 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
 0.000 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 0.134
 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 0.043 0.803

sum of density on p0-p1 =   1.000000
