
seed used = 139980385

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0144.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 308
# site patterns = 107
    2    3    6    4    5    6    5    5    6    4    3    6    1    8   10
    8    9    2    2    2    6   10    1   11    2    1    7    1    3   11
    2    3    1    4    7    2    2   10    9    6    6    2    6    2    5
    1    1    1    7    2    3    1    1    1    1    2    1    1    3    2
    1    1    1    3    3    1    3    1    1    1    1    1    1    1    1
    1    3    3    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    4    1    1    1    1    1    1    1    1    4    1    1
    1    1

1       
K12                   ATG CTC CCG CCT TAT TTT TTG TTC AAA GAG ACA GAC CAG ATT GGC CGC GCC CCC TCT TCC CTT CAT GGC CTG ATC GCC GCG CTC AGC CAG GCT CGG CAA GGT TGG GTA ATA GAA GAT ATC CGT GTT GCA ACT TAC GGT CAC GAT CAA TCG CAC GAC CGT TTA GAA GGA CTA AGT TGC ACC TGT ACG GTG CCA AAC GTG GTC ACG CAA GAC CAG CGC GGG TTC TAC GCT GTT GTG CAT ACA GTG CGT GGG GCT CTG ATT CCA ACA GTA AGG TCG ATT CTG AAT AAG CCA GTA CTA CAA GGG GCA GCA TCA CGG CTT GCC CCC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... AT. ..G ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... AT. ..G ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ..T ... ..T ..T ... ..T ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ..C T.. ..C ... ... ... C.. ..C ... ..G ... ... ... ... ... ..C ... .AT ... ... ..A ... ..C ..G ..T .T. ..A ..T ..T ..T ..G ..G ... ..C .GC ..C ..C ... ..A T.. ..C ..G ..G ..G C.. ... ..C T.A ... ... ..G ..G T.. ..T ..T .T. A.. ... AC. ..G ... ..T 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ..T ..T ... ..T ... ... ... ... ..C ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..T ..T ..T ..G ..G ... ..C .GC ..C ..C ... ..A T.. ..C ..G ... ..G C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..T 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ..T ..T ... ..T ... ... ... ... ..C ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..T ..T ..T ..G ..G ... ..C .GC ..C ..C ... ..A T.. ..C ..G ... ..G C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..T 

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

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

#1: K12            
position  1:    T:0.16558    C:0.33442    A:0.16883    G:0.33117
position  2:    T:0.27273    C:0.22727    A:0.31169    G:0.18831
position  3:    T:0.27597    C:0.27922    A:0.19481    G:0.25000

#2: S2457T         
position  1:    T:0.16234    C:0.33442    A:0.17208    G:0.33117
position  2:    T:0.27922    C:0.22727    A:0.30844    G:0.18506
position  3:    T:0.27273    C:0.27597    A:0.19805    G:0.25325

#3: Shig4337       
position  1:    T:0.16234    C:0.33442    A:0.17208    G:0.33117
position  2:    T:0.27922    C:0.22727    A:0.30844    G:0.18506
position  3:    T:0.27273    C:0.27597    A:0.19805    G:0.25325

#4: CFT073         
position  1:    T:0.17857    C:0.32468    A:0.17208    G:0.32468
position  2:    T:0.27597    C:0.22403    A:0.31169    G:0.18831
position  3:    T:0.27922    C:0.28571    A:0.17208    G:0.26299

#5: O157           
position  1:    T:0.16883    C:0.33766    A:0.16558    G:0.32792
position  2:    T:0.27273    C:0.22403    A:0.31169    G:0.19156
position  3:    T:0.28247    C:0.27273    A:0.18182    G:0.26299

#6: EDL933         
position  1:    T:0.16883    C:0.33766    A:0.16558    G:0.32792
position  2:    T:0.27273    C:0.22403    A:0.31169    G:0.19156
position  3:    T:0.28247    C:0.27273    A:0.18182    G:0.26299

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      39 | Ser S TCT      12 | Tyr Y TAT      33 | Cys C TGT       3
      TTC      33 |       TCC      12 |       TAC      34 |       TGC      21
Leu L TTA       8 |       TCA      24 | *** * TAA       0 | *** * TGA       0
      TTG      33 |       TCG      16 |       TAG       0 | Trp W TGG      42
------------------------------------------------------------------------------
Leu L CTT      42 | Pro P CCT      27 | His H CAT      64 | Arg R CGT      44
      CTC      21 |       CCC      15 |       CAC      32 |       CGC      55
      CTA      11 |       CCA      26 | Gln Q CAA      56 |       CGA       3
      CTG      80 |       CCG      42 |       CAG      75 |       CGG      24
------------------------------------------------------------------------------
Ile I ATT      68 | Thr T ACT      12 | Asn N AAT      24 | Ser S AGT       6
      ATC      46 |       ACC      13 |       AAC      18 |       AGC      21
      ATA       6 |       ACA      27 | Lys K AAA      36 | Arg R AGA       0
Met M ATG      14 |       ACG      13 |       AAG       6 |       AGG       3
------------------------------------------------------------------------------
Val V GTT      21 | Ala A GCT      21 | Asp D GAT      61 | Gly G GGT      36
      GTC      21 |       GCC      61 |       GAC      45 |       GGC      64
      GTA      22 |       GCA      51 | Glu E GAA      65 |       GGA      12
      GTG      44 |       GCG      45 |       GAG      25 |       GGG      14
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16775    C:0.33387    A:0.16937    G:0.32900
position  2:    T:0.27543    C:0.22565    A:0.31061    G:0.18831
position  3:    T:0.27760    C:0.27706    A:0.18777    G:0.25758

Codon frequencies under model, for use in evolver:
  0.01321090  0.01318515  0.00893603  0.01225807
  0.01082308  0.01080198  0.00732087  0.01004246
  0.01489795  0.01486891  0.00000000  0.00000000
  0.00903221  0.00901460  0.00000000  0.00838076
  0.02629395  0.02624270  0.01778558  0.02439751
  0.02154141  0.02149942  0.01457090  0.01998774
  0.02965173  0.02959393  0.02005682  0.02751310
  0.01797701  0.01794196  0.01215989  0.01668042
  0.01333875  0.01331275  0.00902251  0.01237669
  0.01092782  0.01090651  0.00739172  0.01013965
  0.01504212  0.01501280  0.01017469  0.01395722
  0.00911962  0.00910184  0.00616863  0.00846187
  0.02591041  0.02585990  0.01752615  0.02404163
  0.02122719  0.02118582  0.01435836  0.01969619
  0.02921921  0.02916225  0.01976426  0.02711178
  0.01771478  0.01768025  0.01198251  0.01643711



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               0.4561 (0.0050 0.0111)
Shig4337             0.4561 (0.0050 0.0111)-1.0000 (0.0000 0.0000)
CFT073               0.0735 (0.0167 0.2271) 0.0752 (0.0160 0.2122) 0.0752 (0.0160 0.2122)
O157                 0.0398 (0.0050 0.1267) 0.0724 (0.0101 0.1398) 0.0724 (0.0101 0.1398) 0.1544 (0.0145 0.0938)
EDL933               0.0398 (0.0050 0.1267) 0.0724 (0.0101 0.1398) 0.0724 (0.0101 0.1398) 0.1544 (0.0145 0.0938)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 59
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1568.300202     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00003  0.00000  0.02280  0.00000  0.00000  0.12899  0.12220  0.00469  0.00000  0.00000  1.46263  0.89697  0.09957  0.00000 38.88178
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.27872

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.022795): 0.000034, (4: 0.122196, (5: 0.000004, 6: 0.000004): 0.004689): 0.128989);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.022795): 0.000034, (CFT073: 0.122196, (O157: 0.000004, EDL933: 0.000004): 0.004689): 0.128989);

Detailed output identifying parameters

kappa (ts/tv) =  1.46263


dN/dS for site classes (K=3)

p:   0.89697  0.09957  0.00346
w:   0.00000  1.00000 38.88178

dN & dS for each branch

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

   7..8       0.000    254.3    669.7   0.2342   0.0000   0.0000    0.0    0.0
   8..1       0.000    254.3    669.7   0.2342   0.0000   0.0000    0.0    0.0
   8..9       0.023    254.3    669.7   0.2342   0.0040   0.0171    4.3    2.7
   9..2       0.000    254.3    669.7   0.2342   0.0000   0.0000    0.0    0.0
   9..3       0.000    254.3    669.7   0.2342   0.0000   0.0000    0.0    0.0
   7..10      0.129    254.3    669.7   0.2342   0.0226   0.0966   24.6   15.2
  10..4       0.122    254.3    669.7   0.2342   0.0214   0.0915   23.3   14.4
  10..11      0.005    254.3    669.7   0.2342   0.0008   0.0035    0.9    0.6
  11..5       0.000    254.3    669.7   0.2342   0.0000   0.0000    0.0    0.0
  11..6       0.000    254.3    669.7   0.2342   0.0000   0.0000    0.0    0.0


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

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

   289 R      0.987*        38.394


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

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

   131 V      0.552         3.090 +- 2.908
   155 Q      0.776         4.265 +- 2.748
   196 T      0.590         3.334 +- 2.995
   289 R      0.971*        5.117 +- 2.440



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.066  0.137  0.170  0.160  0.133  0.105  0.081  0.062  0.048  0.038

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 0.006
 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 0.988

sum of density on p0-p1 =   1.000000
