
seed used = 139989093

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0208.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 304
# site patterns = 84
    8    8    6    9    2   18    2    9    6    2    1    6    9    4    4
    6    7    5    7    4    3    4    4    8    5    9    1    5    5    2
    1    6    7    5    5    3    6    3    5    5    1    1    8    7    3
    4    1    1    1    1    1    1    8    1    1    1    2    1    1    5
    1    3    1    3    4    3    1    2    1    3    4    1    1    1    1
    1    1    1    1    1    1    1    1    1

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

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

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

#1: K12            
position  1:    T:0.17763    C:0.20724    A:0.27961    G:0.33553
position  2:    T:0.30263    C:0.23684    A:0.26645    G:0.19408
position  3:    T:0.23355    C:0.24671    A:0.24671    G:0.27303

#2: S2457T         
position  1:    T:0.18092    C:0.20724    A:0.28289    G:0.32895
position  2:    T:0.30921    C:0.23355    A:0.26316    G:0.19408
position  3:    T:0.23026    C:0.24671    A:0.25000    G:0.27303

#3: Shig4337       
position  1:    T:0.18092    C:0.20724    A:0.28289    G:0.32895
position  2:    T:0.30921    C:0.23355    A:0.26316    G:0.19408
position  3:    T:0.23026    C:0.24671    A:0.25000    G:0.27303

#4: CFT073         
position  1:    T:0.18421    C:0.20066    A:0.28289    G:0.33224
position  2:    T:0.30263    C:0.23684    A:0.26645    G:0.19408
position  3:    T:0.23355    C:0.24342    A:0.25000    G:0.27303

#5: O157           
position  1:    T:0.18092    C:0.20395    A:0.27303    G:0.34211
position  2:    T:0.30263    C:0.23684    A:0.26316    G:0.19737
position  3:    T:0.23684    C:0.24671    A:0.24013    G:0.27632

#6: EDL933         
position  1:    T:0.18092    C:0.20395    A:0.27303    G:0.34211
position  2:    T:0.30263    C:0.23684    A:0.26316    G:0.19737
position  3:    T:0.23684    C:0.24671    A:0.24013    G:0.27632

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      39 | Ser S TCT       0 | Tyr Y TAT      32 | Cys C TGT      11
      TTC      21 |       TCC      48 |       TAC      22 |       TGC      13
Leu L TTA      54 |       TCA      25 | *** * TAA       0 | *** * TGA       0
      TTG      42 |       TCG      17 |       TAG       0 | Trp W TGG       6
------------------------------------------------------------------------------
Leu L CTT      30 | Pro P CCT       6 | His H CAT      18 | Arg R CGT      43
      CTC      12 |       CCC      18 |       CAC       6 |       CGC      37
      CTA       6 |       CCA      24 | Gln Q CAA      30 |       CGA       7
      CTG      54 |       CCG      32 |       CAG      18 |       CGG      33
------------------------------------------------------------------------------
Ile I ATT      56 | Thr T ACT      18 | Asn N AAT      30 | Ser S AGT      34
      ATC      50 |       ACC      12 |       AAC      18 |       AGC      58
      ATA      10 |       ACA      18 | Lys K AAA      52 | Arg R AGA      13
Met M ATG      50 |       ACG      54 |       AAG      30 |       AGG       6
------------------------------------------------------------------------------
Val V GTT      16 | Ala A GCT      35 | Asp D GAT      46 | Gly G GGT      12
      GTC      40 |       GCC      44 |       GAC      26 |       GGC      24
      GTA      28 |       GCA      37 | Glu E GAA     110 |       GGA      35
      GTG      48 |       GCG      42 |       GAG      44 |       GGG      24
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.18092    C:0.20504    A:0.27906    G:0.33498
position  2:    T:0.30482    C:0.23575    A:0.26425    G:0.19518
position  3:    T:0.23355    C:0.24616    A:0.24616    G:0.27412

Codon frequencies under model, for use in evolver:
  0.01332760  0.01404717  0.01404717  0.01564272
  0.01030732  0.01086381  0.01086381  0.01209779
  0.01155378  0.01217758  0.00000000  0.00000000
  0.00853350  0.00899423  0.00000000  0.01001584
  0.01510461  0.01592012  0.01592012  0.01772842
  0.01168163  0.01231232  0.01231232  0.01371083
  0.01309429  0.01380126  0.01380126  0.01536888
  0.00967130  0.01019346  0.01019346  0.01135129
  0.02055681  0.02166669  0.02166669  0.02412772
  0.01589826  0.01675661  0.01675661  0.01865992
  0.01782083  0.01878299  0.01878299  0.02091647
  0.01316228  0.01387292  0.01387292  0.01544868
  0.02467625  0.02600854  0.02600854  0.02896274
  0.01908415  0.02011452  0.02011452  0.02239924
  0.02139200  0.02254697  0.02254697  0.02510799
  0.01579990  0.01665295  0.01665295  0.01854449



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               0.4254 (0.0159 0.0374)
Shig4337             0.4254 (0.0159 0.0374)-1.0000 (0.0000 0.0000)
CFT073               0.1369 (0.0044 0.0319) 0.3354 (0.0174 0.0518) 0.3354 (0.0174 0.0518)
O157                 0.1600 (0.0058 0.0365) 0.2819 (0.0159 0.0564) 0.2819 (0.0159 0.0564) 0.3218 (0.0073 0.0227)
EDL933               0.1600 (0.0058 0.0365) 0.2819 (0.0159 0.0564) 0.2819 (0.0159 0.0564) 0.3218 (0.0073 0.0227)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 25
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 10  np: 15):  -1433.380973     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.01124  0.01048  0.06308  0.00000  0.00000  0.00001  0.01400  0.02052  0.00000  0.00000  4.43584  0.95357  0.00000  0.02611 12.47967
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.11934

((1: 0.010479, (2: 0.000004, 3: 0.000004): 0.063081): 0.011236, (4: 0.013996, (5: 0.000004, 6: 0.000004): 0.020523): 0.000011);

((K12: 0.010479, (S2457T: 0.000004, Shig4337: 0.000004): 0.063081): 0.011236, (CFT073: 0.013996, (O157: 0.000004, EDL933: 0.000004): 0.020523): 0.000011);

Detailed output identifying parameters

kappa (ts/tv) =  4.43584


dN/dS for site classes (K=3)

p:   0.95357  0.00000  0.04643
w:   0.02611  1.00000 12.47967

dN & dS for each branch

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

   7..8       0.011    276.2    635.8   0.6043   0.0031   0.0052    1.4    2.0
   8..1       0.010    276.2    635.8   0.6043   0.0029   0.0048    1.3    1.9
   8..9       0.063    276.2    635.8   0.6043   0.0175   0.0290    8.0   11.2
   9..2       0.000    276.2    635.8   0.6043   0.0000   0.0000    0.0    0.0
   9..3       0.000    276.2    635.8   0.6043   0.0000   0.0000    0.0    0.0
   7..10      0.000    276.2    635.8   0.6043   0.0000   0.0000    0.0    0.0
  10..4       0.014    276.2    635.8   0.6043   0.0039   0.0064    1.8    2.5
  10..11      0.021    276.2    635.8   0.6043   0.0057   0.0094    2.6    3.6
  11..5       0.000    276.2    635.8   0.6043   0.0000   0.0000    0.0    0.0
  11..6       0.000    276.2    635.8   0.6043   0.0000   0.0000    0.0    0.0


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

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

   175 R      0.902         11.265
   189 I      1.000**       12.475
   192 G      0.875         10.917
   204 I      0.772         9.636
   206 R      0.911         11.376
   246 K      0.851         10.624
   300 A      0.856         10.685
   301 V      0.979*        12.214
   302 R      0.998**       12.451
   303 E      1.000**       12.480
   304 A      1.000**       12.476


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

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

   175 R      0.556         5.053 +- 4.235
   189 I      0.918         8.030 +- 2.728
   192 G      0.512         4.678 +- 4.233
   206 R      0.572         5.188 +- 4.228
   301 V      0.787         6.967 +- 3.646
   302 R      0.927         8.107 +- 2.674
   303 E      0.985*        8.527 +- 2.013
   304 A      0.933         8.141 +- 2.598



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:   0.690  0.239  0.058  0.011  0.002  0.000  0.000  0.000  0.000  0.000
w2:   0.002  0.005  0.013  0.027  0.051  0.085  0.128  0.178  0.230  0.281

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 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.015
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.009 0.066
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.052 0.209
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.012 0.228 0.399

sum of density on p0-p1 =   1.000000
