
seed used = 140015561

K12                                  ATG GCA CTC AAC ACC TAT CAG TAC AGG GAA ACT ACA ATG ATT GAC CCG AAA AAA ATT GAG CAA ATC GCT CGC CAG GTT CAC GAA TCA ATG CCT AAA GGA ATC AGG GAG TTC GGG GAA GAT GTG GAG AAA AAA ATC CGC CAA ACC CTA CAA GCG CAG CTG ACG CGC CTC GAC CTT GTA AGC CGT GAA GAG TTC GAC GTC CAA ACG CAA GTC CTG TTA CGG ACT CGT GAA AAA CTG GCG CTG CTT GAA CAA AGA ATC AGC GAA CTG GAA AAT CGC AGT ACT GAG ATC AAA AAG CAG CCA GAT CCA GAG ACT CTC CCC CCA ACG CTG 
S2457T                               ATG GTA CTC AAC ACC TAT CAG TAC AGG GAA ACT ACA ATG ATT GAC CCG AAA AAA ATT GAG CAA ATC GCT CGC CAG GTT CAC GAA TCA ATG CCT AAA GGA ATC AGG GAG TTC GGG GAA GAT GTG GAG AAA AAA ATC CGC CAA ACC CTA CAA GCT CAG CTG ACG CGC CTC GAC CTT GTA AGC CGT GAA GAG TTC GAC GTC CAA ACG CAA GTC CTG TTA CGG ACT CGT GAG AAA CTG GCG CTG CTT GAA CAA AGA ATC AGC GAA CTG GAA AAT CGC AGT ACT GAG ATC AAA AAG CAG CCA GAT CCA GAG ACT CTC CCC CCA ACG CTG 
Shig4337                             ATG GTA CTC AAC ACC TAT CAG TAC AGG GAA ACT ACA ATG ATT GAC CCG AAA AAA ATT GAG CAA ATC GCT CGC CAG GTT CAC GAA TCA ATG CCT AAA GGA ATC AGG GAG TTC GGG GAA GAT GTG GAG AAA AAA ATC CGC CAA ACC CTA CAA GCT CAG CTG ACG CGC CTC GAC CTT GTA AGC CGT GAA GAG TTC GAC GTC CAA ACG CAA GTC CTG TTA CGG ACT CGT GAG AAA CTG GCG CTG CTT GAA CAA AGA ATC AGC GAA CTG GAA AAT CGC AGT ACT GAG ATC AAA AAG CAG CCA GAT CCA GAG ACT CTC CCC CCA ACG CTG 
CFT073                               ATG GCA CTC AAC ACC TAT CAG TAC AGG GAA ACT ACA ATG ATT GAC CCG AAA AAA ATT GAG CAA ATC GCT CGC CAG GTT CAC GAA TCA ATG CCT AAA GGA ATC AGG GAG TTC GGG GAA GAT GTG GAG AAA AAA ATC CGC CAA ACC CTA CAA GCG CAG CTG ACG CGT CTC GAT CTG GTG AGC CGC GAA GAA TTC GAC GTA CAG ACG CAA GTC CTG TTA CGG ACT CGT GAA AAA CTG GCG TTA CTG GAG CAG CGC ATC AGC GAA CTG GAA GCG CGC TAT AAT CCG GTA GCA GAA CTT CAA TCT CCT CCG GCT ATC CCG CCA GTT GAT 
O157                                 ATG GCA CTC AAC ACC TAT CAG TAC AGG GAA ACT ACA ATG ATT GAC CCG AAA AAA ATT GAG CAA ATC GCT CGC CAG GTT CAC GAA TCA ATG CCT AAA GGA ATC AGG GAG TTC GGG GAA GAT GTG GAG AAA AAA ATC CGC CAA ACC CTA CAA GCG CAG CTG ACG CGT CTC GAT CTG GTA AGC CGC GAA GAA TTC GAC GTT CAG ACG CAA GTC CTG TTG CGG ACT CGT GAA AAA CTG GCG TTA CTG GAG CAG CGC AGC AGT GAA CTG GAA GCG CGC AAT AAT TCG GTA GCA GAT CTT CAA TCT CCT CCG GCT ATC CCG CCT ATT GAT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3042.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 108
# site patterns = 72
    3    1    2    1    2    1    3    1    2    6    2    1    2    2    1
    6    3    4    3    1    3    1    1    1    1    1    2    1    1    1
    1    1    4    2    1    1    2    1    1    1    1    1    2    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1

1       
K12                   ATG GCA CTC AAC ACC TAT CAG TAC AGG GAA ACT ACA ATT GAC CCG AAA GAG CAA ATC GCT CGC GTT CAC TCA CCT GGA TTC GGG GAT GTG CTA GCG CTG ACG CGC GAC CTT GTA AGC CGT GAG GTC CAA GTC TTA CGG CGT GAA GCG CTG GAA AGA ATC AGC AAT AGT ACT GAG ATC AAA AAG CAG CCA GAT CCA GAG ACT CTC CCC CCA ACG CTG 
S2457T                ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
Shig4337              ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..T ..G ..G ... ..C ..A ..A ..G ... ... ... ... ... ... T.A ..G C.C ... ... GCG TA. .A. CC. G.A GC. G.A .TT .A. TC. ..T CC. G.. A.. ..G ... GTT GAT 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..T ..G ... ... ..C ..A ..T ..G ... ..G ... ... ... ... T.A ..G C.C .G. ..T GCG .A. .A. TC. G.A GC. G.T .TT .A. TC. ..T CC. G.. A.. ..G ..T .TT GAT 

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

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

#1: K12            
position  1:    T:0.05556    C:0.33333    A:0.33333    G:0.27778
position  2:    T:0.27778    C:0.19444    A:0.38889    G:0.13889
position  3:    T:0.16667    C:0.25000    A:0.29630    G:0.28704

#2: S2457T         
position  1:    T:0.05556    C:0.33333    A:0.33333    G:0.27778
position  2:    T:0.28704    C:0.18519    A:0.38889    G:0.13889
position  3:    T:0.17593    C:0.25000    A:0.28704    G:0.28704

#3: Shig4337       
position  1:    T:0.05556    C:0.33333    A:0.33333    G:0.27778
position  2:    T:0.28704    C:0.18519    A:0.38889    G:0.13889
position  3:    T:0.17593    C:0.25000    A:0.28704    G:0.28704

#4: CFT073         
position  1:    T:0.08333    C:0.33333    A:0.26852    G:0.31481
position  2:    T:0.28704    C:0.21296    A:0.37037    G:0.12963
position  3:    T:0.18519    C:0.22222    A:0.28704    G:0.30556

#5: O157           
position  1:    T:0.08333    C:0.32407    A:0.28704    G:0.30556
position  2:    T:0.27778    C:0.21296    A:0.37037    G:0.13889
position  3:    T:0.22222    C:0.21296    A:0.25926    G:0.30556

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       0 | Ser S TCT       2 | Tyr Y TAT       6 | Cys C TGT       0
      TTC      10 |       TCC       0 |       TAC       5 |       TGC       0
Leu L TTA       6 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG       1 |       TCG       1 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       8 | Pro P CCT       8 | His H CAT       0 | Arg R CGT      10
      CTC      13 |       CCC       3 |       CAC       5 |       CGC      22
      CTA       5 |       CCA      10 | Gln Q CAA      28 |       CGA       0
      CTG      30 |       CCG      10 |       CAG      22 |       CGG       5
------------------------------------------------------------------------------
Ile I ATT      11 | Thr T ACT      16 | Asn N AAT       6 | Ser S AGT       4
      ATC      24 |       ACC      10 |       AAC       5 |       AGC      10
      ATA       0 |       ACA       5 | Lys K AAA      33 | Arg R AGA       3
Met M ATG      15 |       ACG      13 |       AAG       3 |       AGG      10
------------------------------------------------------------------------------
Val V GTT       7 | Ala A GCT       9 | Asp D GAT      13 | Gly G GGT       0
      GTC       8 |       GCC       0 |       GAC      13 |       GGC       0
      GTA       9 |       GCA       5 | Glu E GAA      39 |       GGA       5
      GTG       6 |       GCG      10 |       GAG      28 |       GGG       5
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.06667    C:0.33148    A:0.31111    G:0.29074
position  2:    T:0.28333    C:0.19815    A:0.38148    G:0.13704
position  3:    T:0.18519    C:0.23704    A:0.28333    G:0.29444

Codon frequencies under model, for use in evolver:
  0.00355946  0.00455611  0.00544597  0.00565954
  0.00248929  0.00318630  0.00380862  0.00395798
  0.00479247  0.00613437  0.00000000  0.00000000
  0.00172157  0.00220361  0.00000000  0.00273729
  0.01769842  0.02265398  0.02707858  0.02814049
  0.01237733  0.01584298  0.01893731  0.01967995
  0.02382925  0.03050144  0.03645875  0.03788850
  0.00856002  0.01095683  0.01309683  0.01361043
  0.01661081  0.02126184  0.02541454  0.02641119
  0.01161671  0.01486939  0.01777357  0.01847057
  0.02236488  0.02862705  0.03421827  0.03556016
  0.00803399  0.01028350  0.01229200  0.01277404
  0.01552320  0.01986969  0.02375049  0.02468188
  0.01085609  0.01389580  0.01660982  0.01726119
  0.02090051  0.02675266  0.03197778  0.03323182
  0.00750795  0.00961018  0.01148717  0.01193764



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               0.1508 (0.0040 0.0268)
Shig4337             0.1508 (0.0040 0.0268)-1.0000 (0.0000 0.0000)
CFT073               0.3436 (0.1119 0.3255) 0.3178 (0.1166 0.3667) 0.3178 (0.1166 0.3667)
O157                 0.3313 (0.1132 0.3417) 0.3070 (0.1179 0.3841) 0.3070 (0.1179 0.3841) 0.3052 (0.0206 0.0674)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 42
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):   -653.557095     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00000  0.00000  0.02837  0.00000  0.00000  0.65664  0.03555  0.07323  1.33756  0.81657  0.00000  0.00000  3.36050
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.79380

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.028375): 0.000000, (4: 0.035547, 5: 0.073228): 0.656639);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.028375): 0.000000, (CFT073: 0.035547, O157: 0.073228): 0.656639);

Detailed output identifying parameters

kappa (ts/tv) =  1.33756


dN/dS for site classes (K=3)

p:   0.81657  0.00000  0.18343
w:   0.00000  1.00000  3.36050

dN & dS for each branch

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

   6..7       0.000     80.1    243.9   0.6164   0.0000   0.0000    0.0    0.0
   7..1       0.000     80.1    243.9   0.6164   0.0000   0.0000    0.0    0.0
   7..8       0.028     80.1    243.9   0.6164   0.0082   0.0133    1.1    2.0
   8..2       0.000     80.1    243.9   0.6164   0.0000   0.0000    0.0    0.0
   8..3       0.000     80.1    243.9   0.6164   0.0000   0.0000    0.0    0.0
   6..9       0.657     80.1    243.9   0.6164   0.1897   0.3077   24.7   46.3
   9..4       0.036     80.1    243.9   0.6164   0.0103   0.0167    1.3    2.5
   9..5       0.073     80.1    243.9   0.6164   0.0212   0.0343    2.8    5.2


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

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

     2 A      1.000**       3.360
    85 I      1.000**       3.360
    90 N      1.000**       3.361
    92 S      1.000**       3.361
    93 T      1.000**       3.360
    94 E      1.000**       3.361
    95 I      1.000**       3.360
    96 K      1.000**       3.361
    97 K      1.000**       3.361
    98 Q      1.000**       3.360
    99 P      1.000**       3.360
   100 D      1.000**       3.361
   102 E      1.000**       3.361
   103 T      1.000**       3.360
   104 L      1.000**       3.360
   107 T      1.000**       3.361
   108 L      1.000**       3.361


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

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

    90 N      0.906         4.709 +- 2.055
    92 S      0.866         4.545 +- 2.159
    94 E      0.949         4.933 +- 1.960
    96 K      0.763         4.000 +- 2.244
    97 K      0.839         4.404 +- 2.197
    98 Q      0.614         3.263 +- 2.466
   100 D      0.887         4.638 +- 2.111
   102 E      0.772         4.044 +- 2.239
   107 T      0.943         4.913 +- 1.985
   108 L      0.898         4.671 +- 2.069



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:   0.960  0.039  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.005  0.076  0.207  0.245  0.192  0.123  0.072  0.041  0.024  0.014

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 0.001 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005 0.013 0.017
 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 0.011 0.087 0.088 0.023
 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 0.003 0.036 0.154 0.426 0.128 0.003

sum of density on p0-p1 =   1.000000
