
seed used = 140003005

K12                                  ATG ACA ATC ACG GAC CTG GTA CTG ATT CTT TTC ATC GCC GCA CTC CTG GCC TTC GCG ATC TAC GAT CAG TTC ATC ATG CCC CGC CGT AAC GGC CCC ACC CTG CTG GCA ATT CCT TTG CTC CGG CGT GGT CGC ATC GAT AGC GTT ATC TTC GTC GGA TTG ATT GTC ATT CTT ATC TAT AAC AAC GTC ACG AAT CAT GGT GCG TTA ATA ACG ACA TGG TTA TTA AGC GCA CTG GCT CTG ATG GGT TTT TAT ATA TTC TGG ATC CGC GTT CCG AAG ATC ATC TTT AAA CAA AAA GGT TTT TTC TTC GCC AAT GTC TGG ATT GAA TAT AGC CGA ATC AAA GCG ATG AAC TTG TCG GAA GAT GGC GTG TTG GTG ATG CAA TTA GAA CAG CGT CGG CTG TTA ATC CGC GTT CGA AAT ATC GAC GAT CTG GAA AAA ATT TAT AAG CTT CTC GTT TCA ACT CAA 
S2457T                               ATG ACA ATC ACG GAC CTG GTA CTG ATT CTT TTC ATC GCC GCA CTC CTG GCC TTC GCG ATC TAC GAT CAG TTC ATC ATG CCC CGC CGT AAC GGC CCC ACC CTG CTG GCA ATT CCT TTG CTC CGG CGT GGT CGC ATC GAT AGC GTT ATC TTC GTC GGA TTG ATT GTC ATT CTT ATC TAT AAC AAC GTC ACG AAT CAT GGC GCG CTA ATA ACA ACA TGG TTA TTA AGT GCA CTG GCT CTG ATG GGT TTT TAT ATA TTC TGG ATC CGC ATT CCG AAG ATC ATC TTT AAA CAA AAA GGT TTT TTC TTC GCC AAT GTC TGG ATT GAA TAT AGC CGA ATC AAA GCG ATG AAC TTG TCG GAA GAT GGC GTG TTG GTG ATG CAA TTA GAA CAG CGT CGG CTG TTA ATC CGC GTT CGA AAT ATC GAC GAT CTG GAA AAA ATT TAT AAG CTT CTC GTA TCA GGT AAT 
Shig4337                             ATG ACA ATC ACG GAC CTG GTA CTG ATT CTT TTC ATC GCC GCA CTC CTG GCC TTC GCG ATC TAC GAT CAG TTC ATC ATG CCC CGC CGT AAC GGC CCC ACC CTG CTG GCA ATT CCT TTG CTC CGG CGT GGT CGC ATC GAT AGC GTT ATC TTC GTC GGA TTG ATT GTC ATT CTT ATC TAT AAC AAC GTC ACG AAT CAT GGC GCG CTA ATA ACA ACA TGG TTA TTA AGT GCA CTG GCT CTG ATG GGT TTT TAT ATA TTC TGG ATC CGC ATT CCG AAG ATC ATC TTT AAA CAA AAA GGT TTT TTC TTC GCC AAT GTC TGG ATT GAA TAT AGC CGA ATC AAA GCG ATG AAC TTG TCG GAA GAT GGC GTG TTG GTG ATG CAA TTA GAA CAG CGT CGG CTG TTA ATC CGC GTT CGA AAT ATC GAC GAT CTG GAA AAA ATT TAT AAG CTT CTC GTA TCA GGT AAT 
CFT073                               ATG ACA ATC ACG GAC CTG GTA CTG ATT CTT TTC ATC GCC GCA CTC CTG GCC TTC GCG ATC TAC GAT CAG TTC ATC ATG CCC CGC CGT AAC GGC CCC ACC CTG CTG GCA ATT CCT TTG CTC CGG CGT GGT CGC ATC GAT AGC GTT ATC TTC GTC GGA TTG ATT GTC ATT CTT ATC TAT AAC AAC GTC ACG AAT CAT GGC GCG CTA ATA ACA ACA TGG TTA TTA AGT GCA CTG GCT CTG ATG GGT TTT TAT ATA TTC TGG ATC CGC GTT CCG AAG ATC ATC TTT AAA CAA AAA GGT TTT TTC TTC GCC AAT GTC TGG ATT GAA TAT AGC CGA ATC AAA GCG ATG AAC TTG TCG GAA GAT GGC GTG TTG GTG ATG CAA TTA GAA CAG CGC CGG CTG TTA ATC CGC GTT CGA AAT ATC GAC GAT CTG GAA AAA ATT TAT AAG CTT CTC GTT TCA ACT CAA 
O157                                 ATG ACA ATC ACG GAC CTG GTA CTG ATT CTT TTC ATC GCC GCA CTC CTG GCC TTC GCG ATC TAC GAT CAG TTC ATC ATG CCC CGC CGT AAC GGC CCC ACC CTG CTG GCA ATT CCT TTG CTC CGG CGT GGT CGC ATC GAT AGC GTT ATC TTC GTC GGA TTG ATT GTC ATT CTT ATC TAT AAC AAC GTC ACG AAT CAT GGT GCG TTA ATA ACG ACA TGG TTA TTA AGC GCA CTG GCT CTG ATG GGT TTT TAT ATA TTC TGG ATC CGC GTT CCG AAG ATC ATC TTT AAA CAA AAA GGT TTT TTC TTC GCC AAT GTC TGG ATT GAA TAT AGC CGA ATC AAA GCG ATG AAC TTG TCG GAA GAT GGC GTG TTG GTG ATG CAA TTA GAA CAG CGT CGG CTG TTA ATC CGC GTT CGA AAT ATC GAC GAT CTG GAA AGA ATT TAT AAA CTT CTC GTT TCA ACT CAA 
EDL933                               ATG ACA ATC ACG GAC CTG GTA CTG ATT CTT TTC ATC GCC GCA CTC CTG GCC TTC GCG ATC TAC GAT CAG TTC ATC ATG CCC CGC CGT AAC GGC CCC ACC CTG CTG GCA ATT CCT TTG CTC CGG CGT GGT CGC ATC GAT AGC GTT ATC TTC GTC GGA TTG ATT GTC ATT CTT ATC TAT AAC AAC GTC ACG AAT CAT GGT GCG TTA ATA ACG ACA TGG TTA TTA AGC GCA CTG GCT CTG ATG GGT TTT TAT ATA TTC TGG ATC CGC GTT CCG AAG ATC ATC TTT AAA CAA AAA GGT TTT TTC TTC GCC AAT GTC TGG ATT GAA TAT AGC CGA ATC AAA GCG ATG AAC TTG TCG GAA GAT GGC GTG TTG GTG ATG CAA TTA GAA CAG CGT CGG CTG TTA ATC CGC GTT CGA AAT ATC GAC GAT CTG GAA AGA ATT TAT AAA CTT CTC GTT TCA ACT CAA 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1820.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 152
# site patterns = 59
    5    2   13    2    2    9    1    6    3    7    3    3    3    3    1
    4    2    2    4    2    4    2    1    1    4    2    3    2    2    4
    1    4    3    1    1    1    2    1    3    4    1    1    3    1    1
    1    3    2    4    2    1    2    1    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  3  3  3  3  3  3 | Ser TCT  0  0  0  0  0  0 | Tyr TAT  4  4  4  4  4  4 | Cys TGT  0  0  0  0  0  0
    TTC  7  7  7  7  7  7 |     TCC  0  0  0  0  0  0 |     TAC  1  1  1  1  1  1 |     TGC  0  0  0  0  0  0
Leu TTA  5  4  4  4  5  5 |     TCA  1  1  1  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  4  4  4  4  4  4 |     TCG  1  1  1  1  1  1 |     TAG  0  0  0  0  0  0 | Trp TGG  3  3  3  3  3  3
--------------------------------------------------------------------------------------------------------------
Leu CTT  3  3  3  3  3  3 | Pro CCT  1  1  1  1  1  1 | His CAT  1  1  1  1  1  1 | Arg CGT  3  3  3  2  3  3
    CTC  3  3  3  3  3  3 |     CCC  2  2  2  2  2  2 |     CAC  0  0  0  0  0  0 |     CGC  4  4  4  5  4  4
    CTA  0  1  1  1  0  0 |     CCA  0  0  0  0  0  0 | Gln CAA  3  2  2  3  3  3 |     CGA  2  2  2  2  2  2
    CTG  9  9  9  9  9  9 |     CCG  1  1  1  1  1  1 |     CAG  2  2  2  2  2  2 |     CGG  2  2  2  2  2  2
--------------------------------------------------------------------------------------------------------------
Ile ATT  6  7  7  6  6  6 | Thr ACT  1  0  0  1  1  1 | Asn AAT  3  4  4  3  3  3 | Ser AGT  0  1  1  1  0  0
    ATC 13 13 13 13 13 13 |     ACC  1  1  1  1  1  1 |     AAC  4  4  4  4  4  4 |     AGC  3  2  2  2  3  3
    ATA  2  2  2  2  2  2 |     ACA  2  3  3  3  2  2 | Lys AAA  4  4  4  4  4  4 | Arg AGA  0  0  0  0  1  1
Met ATG  5  5  5  5  5  5 |     ACG  3  2  2  2  3  3 |     AAG  2  2  2  2  1  1 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  4  2  2  4  4  4 | Ala GCT  1  1  1  1  1  1 | Asp GAT  4  4  4  4  4  4 | Gly GGT  4  4  4  3  4  4
    GTC  4  4  4  4  4  4 |     GCC  3  3  3  3  3  3 |     GAC  2  2  2  2  2  2 |     GGC  2  3  3  3  2  2
    GTA  1  2  2  1  1  1 |     GCA  3  3  3  3  3  3 | Glu GAA  4  4  4  4  4  4 |     GGA  1  1  1  1  1  1
    GTG  2  2  2  2  2  2 |     GCG  3  3  3  3  3  3 |     GAG  0  0  0  0  0  0 |     GGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.19079    C:0.23684    A:0.32237    G:0.25000
position  2:    T:0.46711    C:0.15132    A:0.22368    G:0.15789
position  3:    T:0.25000    C:0.32237    A:0.18421    G:0.24342

#2: S2457T         
position  1:    T:0.18421    C:0.23684    A:0.32895    G:0.25000
position  2:    T:0.46711    C:0.14474    A:0.22368    G:0.16447
position  3:    T:0.25000    C:0.32237    A:0.19079    G:0.23684

#3: Shig4337       
position  1:    T:0.18421    C:0.23684    A:0.32895    G:0.25000
position  2:    T:0.46711    C:0.14474    A:0.22368    G:0.16447
position  3:    T:0.25000    C:0.32237    A:0.19079    G:0.23684

#4: CFT073         
position  1:    T:0.18421    C:0.24342    A:0.32237    G:0.25000
position  2:    T:0.46711    C:0.15132    A:0.22368    G:0.15789
position  3:    T:0.24342    C:0.32895    A:0.19079    G:0.23684

#5: O157           
position  1:    T:0.19079    C:0.23684    A:0.32237    G:0.25000
position  2:    T:0.46711    C:0.15132    A:0.21711    G:0.16447
position  3:    T:0.25000    C:0.32237    A:0.19079    G:0.23684

#6: EDL933         
position  1:    T:0.19079    C:0.23684    A:0.32237    G:0.25000
position  2:    T:0.46711    C:0.15132    A:0.21711    G:0.16447
position  3:    T:0.25000    C:0.32237    A:0.19079    G:0.23684

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      18 | Ser S TCT       0 | Tyr Y TAT      24 | Cys C TGT       0
      TTC      42 |       TCC       0 |       TAC       6 |       TGC       0
Leu L TTA      27 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG      24 |       TCG       6 |       TAG       0 | Trp W TGG      18
------------------------------------------------------------------------------
Leu L CTT      18 | Pro P CCT       6 | His H CAT       6 | Arg R CGT      17
      CTC      18 |       CCC      12 |       CAC       0 |       CGC      25
      CTA       3 |       CCA       0 | Gln Q CAA      16 |       CGA      12
      CTG      54 |       CCG       6 |       CAG      12 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      38 | Thr T ACT       4 | Asn N AAT      20 | Ser S AGT       3
      ATC      78 |       ACC       6 |       AAC      24 |       AGC      15
      ATA      12 |       ACA      15 | Lys K AAA      24 | Arg R AGA       2
Met M ATG      30 |       ACG      15 |       AAG      10 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      20 | Ala A GCT       6 | Asp D GAT      24 | Gly G GGT      23
      GTC      24 |       GCC      18 |       GAC      12 |       GGC      15
      GTA       8 |       GCA      18 | Glu E GAA      24 |       GGA       6
      GTG      12 |       GCG      18 |       GAG       0 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.18750    C:0.23794    A:0.32456    G:0.25000
position  2:    T:0.46711    C:0.14912    A:0.22149    G:0.16228
position  3:    T:0.24890    C:0.32346    A:0.18969    G:0.23794

Codon frequencies under model, for use in evolver:
  0.02232486  0.02901248  0.01701410  0.02134138
  0.00712718  0.00926220  0.00543173  0.00681321
  0.01058597  0.01375709  0.00000000  0.00000000
  0.00775605  0.01007945  0.00000000  0.00741438
  0.02833038  0.03681701  0.02159099  0.02708234
  0.00904444  0.01175379  0.00689290  0.00864601
  0.01343365  0.01745783  0.01023798  0.01284186
  0.00984248  0.01279089  0.00750110  0.00940889
  0.03864420  0.05022044  0.02945131  0.03694181
  0.01233712  0.01603282  0.00940229  0.01179363
  0.01832424  0.02381345  0.01396517  0.01751701
  0.01342568  0.01744748  0.01023191  0.01283424
  0.02976648  0.03868331  0.02268547  0.02845518
  0.00950291  0.01234960  0.00724231  0.00908428
  0.01411462  0.01834279  0.01075696  0.01349283
  0.01034141  0.01343927  0.00788134  0.00988584



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               0.3158 (0.0146 0.0464)
Shig4337             0.3158 (0.0146 0.0464)-1.0000 (0.0000 0.0000)
CFT073               0.0000 (0.0000 0.0463) 0.8068 (0.0147 0.0182) 0.8068 (0.0147 0.0182)
O157                 0.3216 (0.0029 0.0090) 0.3151 (0.0176 0.0559) 0.3151 (0.0176 0.0559) 0.0521 (0.0029 0.0558)
EDL933               0.3216 (0.0029 0.0090) 0.3151 (0.0176 0.0559) 0.3151 (0.0176 0.0559) 0.0521 (0.0029 0.0558)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 15
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -699.823010     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.00000  0.08391  0.00000  0.00000  0.00000  0.03766  0.01447  0.00000  0.00000  5.71193  0.96424  0.00000  0.00118 11.45912
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.13606

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.083910): 0.000000, (4: 0.037663, (5: 0.000004, 6: 0.000004): 0.014468): 0.000000);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.083910): 0.000000, (CFT073: 0.037663, (O157: 0.000004, EDL933: 0.000004): 0.014468): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  5.71193


dN/dS for site classes (K=3)

p:   0.96424  0.00000  0.03576
w:   0.00118  1.00000 11.45912

dN & dS for each branch

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

   7..8       0.000    149.1    306.9   0.4109   0.0000   0.0000    0.0    0.0
   8..1       0.000    149.1    306.9   0.4109   0.0000   0.0000    0.0    0.0
   8..9       0.084    149.1    306.9   0.4109   0.0190   0.0463    6.9    5.8
   9..2       0.000    149.1    306.9   0.4109   0.0000   0.0000    0.0    0.0
   9..3       0.000    149.1    306.9   0.4109   0.0000   0.0000    0.0    0.0
   7..10      0.000    149.1    306.9   0.4109   0.0000   0.0000    0.0    0.0
  10..4       0.038    149.1    306.9   0.4109   0.0085   0.0208    3.1    2.6
  10..11      0.014    149.1    306.9   0.4109   0.0033   0.0080    1.2    1.0
  11..5       0.000    149.1    306.9   0.4109   0.0000   0.0000    0.0    0.0
  11..6       0.000    149.1    306.9   0.4109   0.0000   0.0000    0.0    0.0


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

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

    89 V      0.983*        11.267
   143 K      0.991**       11.360
   151 T      1.000**       11.459
   152 Q      1.000**       11.459


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

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

   151 T      0.898         6.662 +- 3.058
   152 Q      0.904         6.706 +- 3.029



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:   0.719  0.211  0.053  0.013  0.003  0.001  0.000  0.000  0.000  0.000
w2:   0.039  0.048  0.062  0.079  0.097  0.113  0.126  0.138  0.146  0.152

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.016
 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 0.011 0.058
 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 0.002 0.006 0.042 0.188
 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 0.002 0.006 0.021 0.146 0.488

sum of density on p0-p1 =   1.000000
