
seed used = 140004777

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2004.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 122
# site patterns = 76
    2    1    6    2    3    6    2    1    1    1    2    2    2    1    2
    4    1    2    2    1    1    1    6    1    3    1    3    1    1    1
    2    3    1    1    1    3    1    1    1    1    1    2    1    1    1
    1    1    2    1    2    2    1    1    1    1    1    1    1    1    1
    2    3    1    1    1    1    1    1    1    2    1    1    1    1    1
    1

1       
K12                   GTG TCA GAC ACA CTC CCC GGG ACA CTT AAT CAC CGC TGG CTG TGC ACC ACG TGT TTC GGG GCA CGT CTG GTG CAG GAG GGT AAC CGG TTG CAT TAC CTT GCC CGC GCC ATC AGA GGC CTG AGC GAT GCA GAT GCG CTG TTT CCG CTG ATG AAA CAA GAA ACC AGC GAA CTG AAT CAT GTC ACG TAT GCA GGG AAA CTC AGC AGT GAT GTT GCT CCC GAA ATG AAA AAT 
S2457T                ... ... ... ... ... ... ... ..G .C. ... ... ... ... ... ... ... ... ... ... ... ..C ..A ... ..A ... ... ... ... ..C C.. ... ... ... ..A ... ... ... ... ... AG. ... ..C .T. ... ... ... ... ... ... ... ... ... ... ..T G.. ... ... ... ... ... ..A ... ..G ... G.. ... G.. TCC .G. ... ... ..G .C. GC. CCC GCA 
Shig4337              ... ... ... ... ... ... ... ..G .C. ... ... ... ... ... ... ... ... ... ... ... ..C ..A ... ..A ... ... ... ... ..C C.. ... ... ... ..A ... ... ... ... ... AG. ... ..C .T. ... ... ... ... ... ... ... ... ... ... ..T G.. ... ... ... ... ... ..A ... ..G ... G.. ... G.. TCC .G. ... ... ..G .C. GC. CCC GCA 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ..C ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ..G ... ..T ... ..C .GC T.. ... ... ... ..G ..A G.. ..G G.. TCC .G. ... ... ... ... ... ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  1  1  1  1  1  1 | Ser TCT  0  0  0  0  0  0 | Tyr TAT  3  3  3  4  3  3 | Cys TGT  2  2  2  2  2  2
    TTC  2  2  2  2  2  2 |     TCC  0  1  1  1  0  0 |     TAC  3  3  3  3  3  3 |     TGC  2  2  2  2  2  2
Leu TTA  0  0  0  0  0  0 |     TCA  1  1  1  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  1  0  0  2  1  1 |     TCG  0  0  0  0  0  0 |     TAG  0  0  0  0  0  0 | Trp TGG  2  2  2  2  2  2
--------------------------------------------------------------------------------------------------------------
Leu CTT  2  1  1  2  2  2 | Pro CCT  0  1  1  0  0  0 | His CAT  3  3  3  2  3  3 | Arg CGT  1  0  0  2  1  1
    CTC  4  4  4  4  4  4 |     CCC  7  7  7  7  7  7 |     CAC  2  2  2  2  2  2 |     CGC  3  4  4  2  3  3
    CTA  0  0  0  1  0  0 |     CCA  0  0  0  0  0  0 | Gln CAA  1  1  1  1  1  1 |     CGA  0  1  1  0  0  0
    CTG 11 11 11  9 10 10 |     CCG  2  3  3  2  3  3 |     CAG  3  3  3  3  3  3 |     CGG  1  0  0  1  1  1
--------------------------------------------------------------------------------------------------------------
Ile ATT  0  0  0  0  0  0 | Thr ACT  0  1  1  0  0  0 | Asn AAT  3  2  2  2  3  3 | Ser AGT  1  0  0  1  1  1
    ATC  1  1  1  1  1  1 |     ACC  5  4  4  5  5  5 |     AAC  1  1  1  1  1  1 |     AGC  3  1  1  2  3  3
    ATA  0  0  0  0  0  0 |     ACA  3  4  4  3  3  3 | Lys AAA  4  2  2  3  4  4 | Arg AGA  1  1  1  1  1  1
Met ATG  3  2  2  3  3  3 |     ACG  3  2  2  3  3  3 |     AAG  0  0  0  0  0  0 |     AGG  0  1  1  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  2  2  2  2  2  2 | Ala GCT  1  1  1  1  1  1 | Asp GAT  4  1  1  3  3  3 | Gly GGT  3  4  4  4  4  4
    GTC  1  1  1  1  1  1 |     GCC  4  4  4  5  4  4 |     GAC  6  8  8  6  6  6 |     GGC  1  3  3  3  1  1
    GTA  0  2  2  0  0  0 |     GCA  3  3  3  1  3  3 | Glu GAA  3  3  3  3  3  3 |     GGA  0  0  0  1  0  0
    GTG  3  2  2  3  3  3 |     GCG  1  3  3  2  1  1 |     GAG  1  1  1  2  1  1 |     GGG  4  4  4  2  4  4
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13934    C:0.32787    A:0.22951    G:0.30328
position  2:    T:0.25410    C:0.24590    A:0.30328    G:0.19672
position  3:    T:0.21311    C:0.36885    A:0.13115    G:0.28689

#2: S2457T         
position  1:    T:0.13934    C:0.33607    A:0.18033    G:0.34426
position  2:    T:0.23770    C:0.28689    A:0.27049    G:0.20492
position  3:    T:0.18033    C:0.39344    A:0.14754    G:0.27869

#3: Shig4337       
position  1:    T:0.13934    C:0.33607    A:0.18033    G:0.34426
position  2:    T:0.23770    C:0.28689    A:0.27049    G:0.20492
position  3:    T:0.18033    C:0.39344    A:0.14754    G:0.27869

#4: CFT073         
position  1:    T:0.16393    C:0.31148    A:0.20492    G:0.31967
position  2:    T:0.25410    C:0.25410    A:0.28689    G:0.20492
position  3:    T:0.21311    C:0.38525    A:0.12295    G:0.27869

#5: O157           
position  1:    T:0.13934    C:0.32787    A:0.22951    G:0.30328
position  2:    T:0.24590    C:0.25410    A:0.29508    G:0.20492
position  3:    T:0.21311    C:0.36885    A:0.13115    G:0.28689

#6: EDL933         
position  1:    T:0.13934    C:0.32787    A:0.22951    G:0.30328
position  2:    T:0.24590    C:0.25410    A:0.29508    G:0.20492
position  3:    T:0.21311    C:0.36885    A:0.13115    G:0.28689

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       6 | Ser S TCT       0 | Tyr Y TAT      19 | Cys C TGT      12
      TTC      12 |       TCC       3 |       TAC      18 |       TGC      12
Leu L TTA       0 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG       0 |       TAG       0 | Trp W TGG      12
------------------------------------------------------------------------------
Leu L CTT      10 | Pro P CCT       2 | His H CAT      17 | Arg R CGT       5
      CTC      24 |       CCC      42 |       CAC      12 |       CGC      19
      CTA       1 |       CCA       0 | Gln Q CAA       6 |       CGA       2
      CTG      62 |       CCG      16 |       CAG      18 |       CGG       4
------------------------------------------------------------------------------
Ile I ATT       0 | Thr T ACT       2 | Asn N AAT      15 | Ser S AGT       4
      ATC       6 |       ACC      28 |       AAC       6 |       AGC      13
      ATA       0 |       ACA      20 | Lys K AAA      19 | Arg R AGA       6
Met M ATG      16 |       ACG      16 |       AAG       0 |       AGG       2
------------------------------------------------------------------------------
Val V GTT      12 | Ala A GCT       6 | Asp D GAT      15 | Gly G GGT      23
      GTC       6 |       GCC      25 |       GAC      40 |       GGC      12
      GTA       4 |       GCA      16 | Glu E GAA      18 |       GGA       1
      GTG      16 |       GCG      11 |       GAG       7 |       GGG      22
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14344    C:0.32787    A:0.20902    G:0.31967
position  2:    T:0.24590    C:0.26366    A:0.28689    G:0.20355
position  3:    T:0.20219    C:0.37978    A:0.13525    G:0.28279

Codon frequencies under model, for use in evolver:
  0.00728576  0.01368541  0.00487358  0.01019022
  0.00781195  0.01467380  0.00522556  0.01092618
  0.00850005  0.01596632  0.00000000  0.00000000
  0.00603099  0.01132848  0.00000000  0.00843524
  0.01665317  0.03128095  0.01113962  0.02329193
  0.01785589  0.03354012  0.01194415  0.02497412
  0.01942869  0.03649444  0.01299622  0.02717391
  0.01378512  0.02589367  0.00922113  0.01928054
  0.01061639  0.01994160  0.00710151  0.01484860
  0.01138313  0.02138183  0.00761439  0.01592100
  0.01238579  0.02326520  0.00828509  0.01732337
  0.00878801  0.01650722  0.00587847  0.01229134
  0.01623684  0.03049892  0.01086113  0.02270963
  0.01740950  0.03270162  0.01164554  0.02434977
  0.01894298  0.03558208  0.01267131  0.02649457
  0.01344049  0.02524633  0.00899060  0.01879853



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               0.3354 (0.0672 0.2004)
Shig4337             0.3354 (0.0672 0.2004)-1.0000 (0.0000 0.0000)
CFT073               0.1656 (0.0260 0.1569) 0.1840 (0.0554 0.3014) 0.1840 (0.0554 0.3014)
O157                -1.0000 (0.0073 0.0000) 0.3364 (0.0673 0.2000) 0.3364 (0.0673 0.2000) 0.1661 (0.0260 0.1565)
EDL933              -1.0000 (0.0073 0.0000) 0.3364 (0.0673 0.2000) 0.3364 (0.0673 0.2000) 0.1661 (0.0260 0.1565)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 43
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -714.524697     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.01016  0.46447  0.00000  0.00000  0.00000  0.23219  0.00900  0.00000  0.00000  4.16054  0.78685  0.17511  0.00000 11.13753
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.71583

((1: 0.010159, (2: 0.000004, 3: 0.000004): 0.464465): 0.000000, (4: 0.232189, (5: 0.000004, 6: 0.000004): 0.009000): 0.000000);

((K12: 0.010159, (S2457T: 0.000004, Shig4337: 0.000004): 0.464465): 0.000000, (CFT073: 0.232189, (O157: 0.000004, EDL933: 0.000004): 0.009000): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  4.16054


dN/dS for site classes (K=3)

p:   0.78685  0.17511  0.03804
w:   0.00000  1.00000 11.13753

dN & dS for each branch

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

   7..8       0.000    102.2    263.8   0.5988   0.0000   0.0000    0.0    0.0
   8..1       0.010    102.2    263.8   0.5988   0.0029   0.0048    0.5    0.8
   8..9       0.464    102.2    263.8   0.5988   0.1304   0.2178   22.3   34.4
   9..2       0.000    102.2    263.8   0.5988   0.0000   0.0000    0.0    0.0
   9..3       0.000    102.2    263.8   0.5988   0.0000   0.0000    0.0    0.0
   7..10      0.000    102.2    263.8   0.5988   0.0000   0.0000    0.0    0.0
  10..4       0.232    102.2    263.8   0.5988   0.0652   0.1089   11.1   17.2
  10..11      0.009    102.2    263.8   0.5988   0.0025   0.0042    0.4    0.7
  11..5       0.000    102.2    263.8   0.5988   0.0000   0.0000    0.0    0.0
  11..6       0.000    102.2    263.8   0.5988   0.0000   0.0000    0.0    0.0


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

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

    53 L      0.581         6.886
   106 S      0.999**       11.126
   121 K      0.908         10.202
   122 N      0.759         8.692


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

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

    53 L      0.695         5.441 +- 3.570
   100 K      0.661         5.169 +- 3.476
   106 S      0.997**       7.596 +- 2.109
   121 K      0.941         7.219 +- 2.550
   122 N      0.863         6.657 +- 2.986



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:   0.917  0.081  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.001  0.011  0.039  0.078  0.114  0.139  0.153  0.158  0.157  0.151

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 0.004
 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 0.010 0.068
 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 0.011 0.134 0.253
 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 0.088 0.338 0.083

sum of density on p0-p1 =   1.000000
