
seed used = 140009989

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2491.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 711
# site patterns = 107
   14   13   16   22    1   14    4    3    6   16   23   14    9   13   13
    2   17    3   12    2   19    9    7   18    6    5   20    8   13   32
   43   12   13   17    6    5    2   27    9   11    9    9    3   14   13
    6   13    5    1    5    8    1    1    7   13    1   15    1    1   11
    5    8    6    3    3    1    3    1    1    1    1    1    1    1    1
    3    2    4    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 TTT GCC CCG CCA CAA GGA ATA ACA ATT GAA GCG GTA AAC CTC GCG GAG CGG TTA GCA CAG AAA CAC GGC AAG TCT CGC TTC ATC CTG --- AGC CTT CAT GTT TAT TAC GAT GTG ACG GCA GTC TCG CGT AGT CTA ACC ACT TCC TGC TGG CGG ATA TCA AAT CAG TTG GTT ATT GAC GCT GGT CGA TGT CCA TGT CCT GAA GAT CTC GCG CTT TCC ATC ACT AGA CCC GGG GCG GGC CTG GAG CTA CGC CGG TTG CGT CTA TTA ACG CGA --- --- --- --- --- ATG CAG CGG CTG GGG ATC TCG GTT CGC GAG GTG 
O157                                 ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ..G ... ... ... ... ... ... ... ... ... ... --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ..C ..T ... ... ..A ... ..G ..C ... ... ... ... ... ... AA. ... ..C ..C .A. T.. ..G A.. G.. ..C ... ... ... ..C ..T T.. ..A ..G ..A ..A C.. ..C ..T ..G ..A ... --- --- --- --- --- ... ... ..T ... ... ... ... ... ... ... ... 
EDL933                               ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ..G ... ... ... ... ... ... ... ... ... ... --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ..C ..T ... ... ..A ... ..G ..C ... ... ... ... ... ... AA. ... ..C ..C .A. T.. ..G A.. G.. ..C ... ... ... ..C ..T T.. ..A ..G ..A ..A C.. ..C ..T ..G ..A ..G AAT GCA GGC GTC TGG GGA TCT ... T.C .C. .GG .GT TG. AAT CT. C.T 



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 13 13 13 | Ser TCT  5  5  6 | Tyr TAT  5  5  5 | Cys TGT  4  3  5
    TTC  8  8  9 |     TCC  2  0  0 |     TAC  2  2  2 |     TGC  5  5  5
Leu TTA 13 12 12 |     TCA  7  7  7 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG 16 17 17 |     TCG  4  5  4 |     TAG  0  0  0 | Trp TGG  8  8  9
--------------------------------------------------------------------------
Leu CTT 14 14 15 | Pro CCT  3  3  3 | His CAT 17 17 17 | Arg CGT 15 15 14
    CTC 14 13 13 |     CCC  2  3  3 |     CAC  7  8  8 |     CGC 22 23 22
    CTA  8  6  6 |     CCA  4  3  3 | Gln CAA 14 15 15 |     CGA  7  9  8
    CTG 34 36 36 |     CCG 22 23 23 |     CAG 21 20 19 |     CGG  6  3  5
--------------------------------------------------------------------------
Ile ATT 17 17 17 | Thr ACT  6  5  5 | Asn AAT 13 14 16 | Ser AGT 13 13 13
    ATC 15 15 14 |     ACC 13 15 15 |     AAC 13 13 13 |     AGC 12 12 12
    ATA  4  3  3 |     ACA  6  7  7 | Lys AAA  9  9  9 | Arg AGA  3  3  3
Met ATG 15 15 14 |     ACG 12 11 11 |     AAG  6  6  6 |     AGG  0  0  1
--------------------------------------------------------------------------
Val GTT  8  7  6 | Ala GCT  5  5  5 | Asp GAT 28 27 27 | Gly GGT  8  9  9
    GTC  9 10 11 |     GCC 16 17 17 |     GAC 11 13 13 |     GGC 19 18 19
    GTA  9  9  9 |     GCA 11 11 12 | Glu GAA 24 24 24 |     GGA  4  4  5
    GTG 10 11 10 |     GCG 18 16 17 |     GAG 19 18 17 |     GGG  5  5  4
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13876    C:0.31674    A:0.23680    G:0.30769
position  2:    T:0.31222    C:0.20513    A:0.28507    G:0.19759
position  3:    T:0.26244    C:0.25641    A:0.18552    G:0.29563

#2: O157           
position  1:    T:0.13575    C:0.31825    A:0.23831    G:0.30769
position  2:    T:0.31071    C:0.20513    A:0.28808    G:0.19608
position  3:    T:0.25943    C:0.26395    A:0.18401    G:0.29261

#3: EDL933         
position  1:    T:0.14072    C:0.31437    A:0.23802    G:0.30689
position  2:    T:0.30689    C:0.20659    A:0.28593    G:0.20060
position  3:    T:0.26347    C:0.26347    A:0.18413    G:0.28892

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      39 | Ser S TCT      16 | Tyr Y TAT      15 | Cys C TGT      12
      TTC      25 |       TCC       2 |       TAC       6 |       TGC      15
Leu L TTA      37 |       TCA      21 | *** * TAA       0 | *** * TGA       0
      TTG      50 |       TCG      13 |       TAG       0 | Trp W TGG      25
------------------------------------------------------------------------------
Leu L CTT      43 | Pro P CCT       9 | His H CAT      51 | Arg R CGT      44
      CTC      40 |       CCC       8 |       CAC      23 |       CGC      67
      CTA      20 |       CCA      10 | Gln Q CAA      44 |       CGA      24
      CTG     106 |       CCG      68 |       CAG      60 |       CGG      14
------------------------------------------------------------------------------
Ile I ATT      51 | Thr T ACT      16 | Asn N AAT      43 | Ser S AGT      39
      ATC      44 |       ACC      43 |       AAC      39 |       AGC      36
      ATA      10 |       ACA      20 | Lys K AAA      27 | Arg R AGA       9
Met M ATG      44 |       ACG      34 |       AAG      18 |       AGG       1
------------------------------------------------------------------------------
Val V GTT      21 | Ala A GCT      15 | Asp D GAT      82 | Gly G GGT      26
      GTC      30 |       GCC      50 |       GAC      37 |       GGC      56
      GTA      27 |       GCA      34 | Glu E GAA      72 |       GGA      13
      GTG      31 |       GCG      51 |       GAG      54 |       GGG      14
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13842    C:0.31645    A:0.23771    G:0.30742
position  2:    T:0.30993    C:0.20562    A:0.28636    G:0.19809
position  3:    T:0.26179    C:0.26128    A:0.18455    G:0.29238

Codon frequencies under model, for use in evolver:
  0.01150607  0.01148402  0.00811156  0.01285064
  0.00763347  0.00761885  0.00538145  0.00852551
  0.01063101  0.01061064  0.00000000  0.00000000
  0.00735420  0.00734011  0.00000000  0.00821360
  0.02630553  0.02625514  0.01854490  0.02937955
  0.01745189  0.01741846  0.01230325  0.01949129
  0.02430495  0.02425839  0.01713452  0.02714518
  0.01681341  0.01678120  0.01185313  0.01877819
  0.01976042  0.01972256  0.01393072  0.02206958
  0.01310966  0.01308455  0.00924206  0.01464163
  0.01825760  0.01822263  0.01287126  0.02039115
  0.01263004  0.01260584  0.00890394  0.01410596
  0.02555514  0.02550618  0.01801588  0.02854147
  0.01695406  0.01692158  0.01195228  0.01893528
  0.02361162  0.02356639  0.01664574  0.02637084
  0.01633379  0.01630249  0.01151501  0.01824252



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                 
O157                 0.0972 (0.0054 0.0551)
EDL933               0.2612 (0.0171 0.0654) 0.8468 (0.0116 0.0138)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  4  np:  9):  -3039.103716     +0.000000
   4..1     4..5     5..2     5..3  
  0.05161  0.00638  0.00143  0.04115  1.52472  0.96569  0.00000  0.00000 12.30337
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.10057

(1: 0.051615, (2: 0.001429, 3: 0.041145): 0.006382);

(K12: 0.051615, (O157: 0.001429, EDL933: 0.041145): 0.006382);

Detailed output identifying parameters

kappa (ts/tv) =  1.52472


dN/dS for site classes (K=3)

p:   0.96569  0.00000  0.03431
w:   0.00000  1.00000 12.30337

dN & dS for each branch

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

   4..1       0.052    582.3   1550.7   0.4221   0.0125   0.0297   17.3   19.4
   4..5       0.006    582.3   1550.7   0.4221   0.0015   0.0037    2.1    2.4
   5..2       0.001    582.3   1550.7   0.4221   0.0003   0.0008    0.5    0.5
   5..3       0.041    582.3   1550.7   0.4221   0.0100   0.0237   13.8   15.5


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

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

   147 S      1.000**       12.303
   254 C      1.000**       12.303
   258 E      1.000**       12.303
   292 L      1.000**       12.303
   302 A      1.000**       12.303
   324 S      1.000**       12.303
   380 I      1.000**       12.303
   700 M      1.000**       12.303
   701 Q      1.000**       12.303
   703 L      1.000**       12.303
   704 G      1.000**       12.303
   705 I      1.000**       12.303
   706 S      1.000**       12.303
   707 V      1.000**       12.303
   708 R      1.000**       12.303
   709 E      1.000**       12.303
   710 V      1.000**       12.303


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

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

   147 S      0.605         5.699 +- 4.392
   254 C      0.967*        8.854 +- 1.991
   258 E      0.506         4.815 +- 4.458
   292 L      0.542         5.131 +- 4.455
   302 A      0.637         5.984 +- 4.332
   324 S      0.634         5.956 +- 4.339
   380 I      0.566         5.352 +- 4.440
   700 M      0.983*        8.981 +- 1.726
   701 Q      0.993**       9.058 +- 1.538
   703 L      0.629         5.915 +- 4.357
   704 G      0.585         5.521 +- 4.420
   705 I      0.960*        8.800 +- 2.088
   706 S      0.927         8.511 +- 2.587
   707 V      0.969*        8.874 +- 1.953
   708 R      0.972*        8.892 +- 1.920
   709 E      0.958*        8.781 +- 2.122
   710 V      0.599         5.649 +- 4.409



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:   0.983  0.017  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.001  0.006  0.022  0.058  0.117  0.192  0.269  0.335

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 0.000
 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 0.028
 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 0.006 0.966

sum of density on p0-p1 =   1.000000
