
seed used = 140025609

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3874.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 322
# site patterns = 87
   12    2    7    8   11    1    8    9    4    6    4   15    4    4    6
    6    4   16    1    6    7   16   11    2    3    3   11    4    7    1
    1    6    4    5    2    3    6    2    4    6    9    7    1    2    4
    1    6    2    1    1    1    8    1    2    2    1    2    1    1    1
    1    1    1    3    1    1    1    2    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1

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



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

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

#1: K12            
position  1:    T:0.24845    C:0.14286    A:0.29503    G:0.31366
position  2:    T:0.40683    C:0.21739    A:0.20497    G:0.17081
position  3:    T:0.27329    C:0.26087    A:0.21118    G:0.25466

#2: S2457T         
position  1:    T:0.25078    C:0.15047    A:0.29154    G:0.30721
position  2:    T:0.41379    C:0.21003    A:0.20063    G:0.17555
position  3:    T:0.26959    C:0.27900    A:0.20690    G:0.24451

#3: Shig4337       
position  1:    T:0.25078    C:0.15047    A:0.29154    G:0.30721
position  2:    T:0.41379    C:0.21003    A:0.20063    G:0.17555
position  3:    T:0.26959    C:0.27900    A:0.20690    G:0.24451

#4: CFT073         
position  1:    T:0.24845    C:0.14596    A:0.29193    G:0.31366
position  2:    T:0.40683    C:0.21739    A:0.20186    G:0.17391
position  3:    T:0.25776    C:0.27950    A:0.21118    G:0.25155

#5: O157           
position  1:    T:0.24845    C:0.14596    A:0.29193    G:0.31366
position  2:    T:0.40373    C:0.22050    A:0.20497    G:0.17081
position  3:    T:0.26708    C:0.26708    A:0.20807    G:0.25776

#6: EDL933         
position  1:    T:0.24845    C:0.14596    A:0.29193    G:0.31366
position  2:    T:0.40373    C:0.22050    A:0.20497    G:0.17081
position  3:    T:0.26708    C:0.26708    A:0.20807    G:0.25776

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     102 | Ser S TCT      12 | Tyr Y TAT      48 | Cys C TGT      18
      TTC      72 |       TCC      12 |       TAC      36 |       TGC      12
Leu L TTA      25 |       TCA      26 | *** * TAA       0 | *** * TGA       0
      TTG      53 |       TCG      28 |       TAG       0 | Trp W TGG      36
------------------------------------------------------------------------------
Leu L CTT      12 | Pro P CCT       6 | His H CAT       6 | Arg R CGT       6
      CTC      24 |       CCC       6 |       CAC       6 |       CGC       6
      CTA      25 |       CCA       7 | Gln Q CAA      29 |       CGA      12
      CTG      73 |       CCG      47 |       CAG      12 |       CGG       6
------------------------------------------------------------------------------
Ile I ATT      96 | Thr T ACT      11 | Asn N AAT      30 | Ser S AGT      36
      ATC      60 |       ACC      57 |       AAC      38 |       AGC       6
      ATA       6 |       ACA      40 | Lys K AAA      76 | Arg R AGA       9
Met M ATG      76 |       ACG      12 |       AAG      10 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      38 | Ala A GCT      32 | Asp D GAT      18 | Gly G GGT      44
      GTC      46 |       GCC      20 |       GAC      24 |       GGC      99
      GTA      36 |       GCA      48 | Glu E GAA      46 |       GGA      17
      GTG      42 |       GCG      52 |       GAG      12 |       GGG      26
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.24922    C:0.14694    A:0.29232    G:0.31153
position  2:    T:0.40810    C:0.21599    A:0.20301    G:0.17290
position  3:    T:0.26739    C:0.27207    A:0.20872    G:0.25182

Codon frequencies under model, for use in evolver:
  0.02810341  0.02859454  0.02193703  0.02646632
  0.01487407  0.01513401  0.01161044  0.01400762
  0.01398020  0.01422451  0.00000000  0.00000000
  0.01190641  0.01211448  0.00000000  0.01121283
  0.01656930  0.01685886  0.01293371  0.01560410
  0.00876950  0.00892276  0.00684532  0.00825866
  0.00824249  0.00838653  0.00643394  0.00776235
  0.00701982  0.00714250  0.00547955  0.00661090
  0.03296296  0.03353901  0.02573031  0.03104279
  0.01744604  0.01775093  0.01361808  0.01642977
  0.01639760  0.01668416  0.01279968  0.01544240
  0.01396522  0.01420928  0.01090101  0.01315172
  0.03512926  0.03574317  0.02742129  0.03308290
  0.01859259  0.01891751  0.01451305  0.01750952
  0.01747524  0.01778064  0.01364087  0.01645727
  0.01488301  0.01514310  0.01161742  0.01401604



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               0.6356 (0.0196 0.0308)
Shig4337             0.6356 (0.0196 0.0308)-1.0000 (0.0000 0.0000)
CFT073               0.0514 (0.0027 0.0532) 0.3423 (0.0167 0.0489) 0.3423 (0.0167 0.0489)
O157                 0.0894 (0.0027 0.0306) 0.5549 (0.0196 0.0353) 0.5549 (0.0196 0.0353) 0.0563 (0.0027 0.0486)
EDL933               0.0894 (0.0027 0.0306) 0.5549 (0.0196 0.0353) 0.5549 (0.0196 0.0353) 0.0563 (0.0027 0.0486)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1502.296875     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00153  0.01406  0.06424  0.00000  0.00000  0.00164  0.03037  0.01354  0.00000  0.00000  2.48071  0.95829  0.00000  0.00000 10.89766
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.12540

((1: 0.014064, (2: 0.000004, 3: 0.000004): 0.064240): 0.001533, (4: 0.030370, (5: 0.000004, 6: 0.000004): 0.013538): 0.001644);

((K12: 0.014064, (S2457T: 0.000004, Shig4337: 0.000004): 0.064240): 0.001533, (CFT073: 0.030370, (O157: 0.000004, EDL933: 0.000004): 0.013538): 0.001644);

Detailed output identifying parameters

kappa (ts/tv) =  2.48071


dN/dS for site classes (K=3)

p:   0.95829  0.00000  0.04171
w:   0.00000  1.00000 10.89766

dN & dS for each branch

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

   7..8       0.002    282.3    683.7   0.4546   0.0004   0.0008    0.2    0.3
   8..1       0.014    282.3    683.7   0.4546   0.0035   0.0076    2.2    2.4
   8..9       0.064    282.3    683.7   0.4546   0.0159   0.0349    9.8   10.8
   9..2       0.000    282.3    683.7   0.4546   0.0000   0.0000    0.0    0.0
   9..3       0.000    282.3    683.7   0.4546   0.0000   0.0000    0.0    0.0
   7..10      0.002    282.3    683.7   0.4546   0.0004   0.0009    0.3    0.3
  10..4       0.030    282.3    683.7   0.4546   0.0075   0.0165    4.7    5.1
  10..11      0.014    282.3    683.7   0.4546   0.0033   0.0074    2.1    2.3
  11..5       0.000    282.3    683.7   0.4546   0.0000   0.0000    0.0    0.0
  11..6       0.000    282.3    683.7   0.4546   0.0000   0.0000    0.0    0.0


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

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

   151 I      1.000**       10.898
   175 K      1.000**       10.898
   184 K      1.000**       10.898
   312 A      1.000**       10.898
   313 E      1.000**       10.898
   317 G      1.000**       10.898
   319 A      1.000**       10.898
   320 M      1.000**       10.898
   321 A      1.000**       10.898
   322 L      1.000**       10.898


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

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

   175 K      0.644         5.796 +- 4.170
   184 K      0.953*        8.337 +- 2.318
   312 A      0.542         4.918 +- 4.278
   313 E      0.947         8.288 +- 2.387
   317 G      0.568         5.143 +- 4.267
   319 A      0.987*        8.595 +- 1.875
   320 M      0.787         6.979 +- 3.636
   321 A      0.949         8.309 +- 2.359
   322 L      0.939         8.229 +- 2.467



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:   0.915  0.080  0.005  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.002  0.008  0.022  0.048  0.088  0.137  0.189  0.236  0.270

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.011
 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 0.007 0.116
 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 0.002 0.098 0.764

sum of density on p0-p1 =   1.000000
