
seed used = 140016869

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3145.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 347
# site patterns = 128
    1    1    1    1    1    1   10    1    2    4    5    7    3    4    3
    8    5    3    1    3    6    7    3    5    8    1    2    1    1    1
    1    1    1    1    2    1    1    2    5    3    3    7    2    7    5
    3    2    2   11    2    4    2    8    3    3    1    2    1    2    1
    1    1    1    1    1    1    1    5    1    1    1    1    1    2    3
    3    2    5    5    6    1    8    6    3    1    4    8    2    5    3
    4    3    3    6    4    3    1    1    2    2    3    1    1    1    3
    2    1    3    5    1    1    1    1    1    2    1    2    1    4    1
    2    1    1    1    1    1    1    1

K12                                  TGC GCT TAT GCC TCC TCA GGA GGG TGT GCC GAC AGC ACT GGT GCG ACA AAT TAC AGT GTG GTT GAT ACG AAC CAG CGG GAG TTT ACC TCT GCA ACG CTA AGT TGG CAA TCC TGC TCT AAG GCA AAA CTT GTC TAT ATG CCC GTA ACC CAT CTC CTG ATT TTA CCA CGA TTC ATA AAC ACG GCT ACC CAA ACG GGT GTT TGC CAG GGT GAT CGT GCG AAC TTT GGC TCG CCG GAT GTT ATT AAG AAT TTT GGA TTC ATC GGT AAG ACC CGC GCC ATG CCA GAC ACT GTA TAT TGT TCA AAA AAC TCG TTG CAA ACA GGG TAC CTG GTC AGG CGA AGA AGT GTG CCC CGT GAA CTC GGC GCA CCT CTT TCC CAT TGG ATC GTG CGG 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ..C ... ... ... ... ... ... ... ... ... ..C ... ..A ..T ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ..C ... ... ... ... ... ... ... ... ... ..C ... ..A ..T ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... 
O157                                 ATG ATC .GG CAG C.T --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... ..C ..A GA. AA. ..A ..C TCC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- .GG A.. ..C ..G .CG GTT ... ..C --- --- --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
EDL933                               ATG ATC .GG CAG C.T --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... ..C ..A GA. AA. ..A ..C TCC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- .GG A.. ..C ..G .CG GTT ... ..C --- --- --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... 



Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  9  9  9  6  6 | Ser TCT  6  6  6  0  0 | Tyr TAT  7  7  7  1  1 | Cys TGT  3  3  3  1  1
    TTC  3  3  3  2  2 |     TCC  3  3  3  2  2 |     TAC  4  4  4  1  1 |     TGC  4  4  4  0  0
Leu TTA  3  3  3  0  0 |     TCA  3  3  3  2  2 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  1  1  1  1  1 |     TCG  4  4  4  1  1 |     TAG  0  0  0  0  0 | Trp TGG  3  3  3  2  2
--------------------------------------------------------------------------------------------------
Leu CTT  3  3  3  1  1 | Pro CCT  2  2  2  3  3 | His CAT  3  3  3  1  1 | Arg CGT  2  2  2  1  1
    CTC  5  5  5  2  2 |     CCC  4  4  4  2  2 |     CAC  0  0  0  0  0 |     CGC  3  3  3  3  3
    CTA  1  1  1  0  0 |     CCA  6  6  6  3  3 | Gln CAA  3  3  3  1  1 |     CGA  2  2  2  1  1
    CTG  5  5  5  3  3 |     CCG  2  2  2  0  0 |     CAG 13 13 13  6  6 |     CGG  2  2  2  1  1
--------------------------------------------------------------------------------------------------
Ile ATT 14 14 14  6  6 | Thr ACT  7  7  7  4  4 | Asn AAT 13 14 14  8  8 | Ser AGT  3  3  3  1  1
    ATC  5  4  4  6  6 |     ACC 18 19 19  6  6 |     AAC 11  8  8  3  3 |     AGC  7  9  9  0  0
    ATA  1  1  1  0  0 |     ACA 11 11 11  5  5 | Lys AAA  9 10 10  4  4 | Arg AGA  1  1  1  2  2
Met ATG  6  7  7  4  4 |     ACG  6  5  5  0  0 |     AAG  6  5  5  3  3 |     AGG  1  1  1  1  1
--------------------------------------------------------------------------------------------------
Val GTT 12 12 12  6  6 | Ala GCT  2  2  2  0  0 | Asp GAT 13 12 12  6  6 | Gly GGT 14 14 14  8  8
    GTC 12 12 12  5  5 |     GCC  9  9  9  4  4 |     GAC 11 12 12  6  6 |     GGC  7  7  7  5  5
    GTA  5  5  5  3  3 |     GCA  5  6  6  1  1 | Glu GAA  2  2  2  2  2 |     GGA 13 13 13  3  3
    GTG  5  5  5  1  1 |     GCG  4  3  3  2  2 |     GAG  2  2  2  2  2 |     GGG  3  3  3  3  3
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.15274    C:0.16138    A:0.34294    G:0.34294
position  2:    T:0.25937    C:0.26513    A:0.27954    G:0.19597
position  3:    T:0.32565    C:0.30548    A:0.18732    G:0.18156

#2: S2457T         
position  1:    T:0.15274    C:0.16138    A:0.34294    G:0.34294
position  2:    T:0.25937    C:0.26513    A:0.27378    G:0.20173
position  3:    T:0.32565    C:0.30548    A:0.19308    G:0.17579

#3: Shig4337       
position  1:    T:0.15274    C:0.16138    A:0.34294    G:0.34294
position  2:    T:0.25937    C:0.26513    A:0.27378    G:0.20173
position  3:    T:0.32565    C:0.30548    A:0.19308    G:0.17579

#4: O157           
position  1:    T:0.12102    C:0.17834    A:0.33758    G:0.36306
position  2:    T:0.29299    C:0.22293    A:0.28025    G:0.20382
position  3:    T:0.33758    C:0.29936    A:0.17197    G:0.19108

#5: EDL933         
position  1:    T:0.12102    C:0.17834    A:0.33758    G:0.36306
position  2:    T:0.29299    C:0.22293    A:0.28025    G:0.20382
position  3:    T:0.33758    C:0.29936    A:0.17197    G:0.19108

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      39 | Ser S TCT      18 | Tyr Y TAT      23 | Cys C TGT      11
      TTC      13 |       TCC      13 |       TAC      14 |       TGC      12
Leu L TTA       9 |       TCA      13 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG      14 |       TAG       0 | Trp W TGG      13
------------------------------------------------------------------------------
Leu L CTT      11 | Pro P CCT      12 | His H CAT      11 | Arg R CGT       8
      CTC      19 |       CCC      16 |       CAC       0 |       CGC      15
      CTA       3 |       CCA      24 | Gln Q CAA      11 |       CGA       8
      CTG      21 |       CCG       6 |       CAG      51 |       CGG       8
------------------------------------------------------------------------------
Ile I ATT      54 | Thr T ACT      29 | Asn N AAT      57 | Ser S AGT      11
      ATC      25 |       ACC      68 |       AAC      33 |       AGC      25
      ATA       3 |       ACA      43 | Lys K AAA      37 | Arg R AGA       7
Met M ATG      28 |       ACG      16 |       AAG      22 |       AGG       5
------------------------------------------------------------------------------
Val V GTT      48 | Ala A GCT       6 | Asp D GAT      49 | Gly G GGT      58
      GTC      46 |       GCC      35 |       GAC      47 |       GGC      31
      GTA      21 |       GCA      19 | Glu E GAA      10 |       GGA      45
      GTG      17 |       GCG      14 |       GAG      10 |       GGG      15
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.14539    C:0.16531    A:0.34170    G:0.34760
position  2:    T:0.26716    C:0.25535    A:0.27675    G:0.20074
position  3:    T:0.32841    C:0.30406    A:0.18672    G:0.18081

Codon frequencies under model, for use in evolver:
  0.01301955  0.01205406  0.00740213  0.00716807
  0.01244410  0.01152128  0.00707496  0.00685125
  0.01348710  0.01248694  0.00000000  0.00000000
  0.00978265  0.00905719  0.00000000  0.00538595
  0.01480396  0.01370613  0.00841663  0.00815049
  0.01414964  0.01310034  0.00804463  0.00779025
  0.01533559  0.01419834  0.00871889  0.00844319
  0.01112341  0.01029853  0.00632410  0.00612413
  0.03059925  0.02833009  0.01739688  0.01684678
  0.02924680  0.02707793  0.01662795  0.01610217
  0.03169812  0.02934747  0.01802163  0.01745177
  0.02299170  0.02128670  0.01307169  0.01265835
  0.03112796  0.02881960  0.01769747  0.01713787
  0.02975214  0.02754580  0.01691526  0.01638039
  0.03224582  0.02985455  0.01833301  0.01775331
  0.02338897  0.02165450  0.01329755  0.01287707



Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
S2457T               0.1944 (0.0038 0.0197)
Shig4337             0.1944 (0.0038 0.0197)-1.0000 (0.0000 0.0000)
O157                 0.5127 (0.0677 0.1320) 0.4949 (0.0707 0.1429) 0.4949 (0.0707 0.1429)
EDL933               0.5127 (0.0677 0.1320) 0.4949 (0.0707 0.1429) 0.4949 (0.0707 0.1429)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1594.535297     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.11386  0.00000  0.02472  0.00000  0.00000  0.36661  0.00000  0.00000  1.56543  0.90933  0.00000  0.00000 13.87328
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.50521

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.024719): 0.113858, (4: 0.000004, 5: 0.000004): 0.366612);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.024719): 0.113858, (O157: 0.000004, EDL933: 0.000004): 0.366612);

Detailed output identifying parameters

kappa (ts/tv) =  1.56543


dN/dS for site classes (K=3)

p:   0.90933  0.00000  0.09067
w:   0.00000  1.00000 13.87328

dN & dS for each branch

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

   6..7       0.114    267.5    773.5   1.2579   0.0401   0.0318    8.5   31.0
   7..1       0.000    267.5    773.5   1.2579   0.0000   0.0000    0.0    0.0
   7..8       0.025    267.5    773.5   1.2579   0.0087   0.0069    1.8    6.7
   8..2       0.000    267.5    773.5   1.2579   0.0000   0.0000    0.0    0.0
   8..3       0.000    267.5    773.5   1.2579   0.0000   0.0000    0.0    0.0
   6..9       0.367    267.5    773.5   1.2579   0.1290   0.1026   27.4   99.8
   9..4       0.000    267.5    773.5   1.2579   0.0000   0.0000    0.0    0.0
   9..5       0.000    267.5    773.5   1.2579   0.0000   0.0000    0.0    0.0


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

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

     1 C      1.000**       13.873
     2 A      1.000**       13.873
     3 Y      1.000**       13.873
     4 A      1.000**       13.873
     5 S      1.000**       13.873
    42 S      1.000**       13.873
    43 A      1.000**       13.873
    46 S      1.000**       13.873
   119 N      1.000**       13.873
   120 N      1.000**       13.873
   127 T      1.000**       13.873
   128 Q      1.000**       13.873
   131 V      1.000**       13.873
   132 C      1.000**       13.873
   283 V      1.000**       13.873
   345 I      1.000**       13.873


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

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

     1 C      0.993**       9.095 +- 1.556
     2 A      0.918         8.465 +- 2.631
     3 Y      0.948         8.722 +- 2.278
     4 A      0.991**       9.077 +- 1.601
     5 S      0.575         5.442 +- 4.343
    42 S      0.948         8.718 +- 2.285
    43 A      0.946         8.706 +- 2.302
    46 S      0.963*        8.844 +- 2.082
   119 N      0.834         7.732 +- 3.432
   120 N      0.834         7.732 +- 3.432
   127 T      0.882         8.149 +- 3.019
   128 Q      0.541         5.139 +- 4.360
   131 V      0.612         5.785 +- 4.320
   132 C      0.964*        8.855 +- 2.063
   283 V      0.610         5.753 +- 4.300



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:   0.916  0.078  0.005  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.001  0.008  0.024  0.057  0.108  0.179  0.264  0.359

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.008 0.005
 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 0.020 0.085 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 0.000 0.000 0.000 0.015 0.307 0.515 0.024

sum of density on p0-p1 =   1.000000
