
seed used = 140005653

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2102.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 272
# site patterns = 111
    4    9    1    1    1    3    3    1    9    1    1    1    5    1    3
    1    2    2    7    3    2    5    4   10    5    4    4    6    8    8
    8    4    1    1    1    7    4    2    4    2    6    1    1    2    3
    3    1    5    8    1    1    3    1    1    1    1    1    1    4    1
    8    6    6    1    1    4    1    1    1    3    2    1    3    1    1
    1    1    2    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    1    1    1    1

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

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

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

#1: K12            
position  1:    T:0.22426    C:0.23529    A:0.23529    G:0.30515
position  2:    T:0.28676    C:0.20221    A:0.31618    G:0.19485
position  3:    T:0.28309    C:0.23162    A:0.20956    G:0.27574

#2: S2457T         
position  1:    T:0.23529    C:0.24265    A:0.23529    G:0.28676
position  2:    T:0.28676    C:0.19485    A:0.30882    G:0.20956
position  3:    T:0.27941    C:0.24632    A:0.20588    G:0.26838

#3: Shig4337       
position  1:    T:0.23529    C:0.24265    A:0.23529    G:0.28676
position  2:    T:0.28676    C:0.19485    A:0.30882    G:0.20956
position  3:    T:0.27941    C:0.24632    A:0.20588    G:0.26838

#4: CFT073         
position  1:    T:0.23162    C:0.23162    A:0.23162    G:0.30515
position  2:    T:0.29044    C:0.19118    A:0.31985    G:0.19853
position  3:    T:0.28309    C:0.23162    A:0.21324    G:0.27206

#5: O157           
position  1:    T:0.21691    C:0.23897    A:0.22794    G:0.31618
position  2:    T:0.28309    C:0.20221    A:0.32353    G:0.19118
position  3:    T:0.27941    C:0.23529    A:0.20956    G:0.27574

#6: EDL933         
position  1:    T:0.21691    C:0.23897    A:0.22794    G:0.31618
position  2:    T:0.28309    C:0.20221    A:0.32353    G:0.19118
position  3:    T:0.27941    C:0.23529    A:0.20956    G:0.27574

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      48 | Ser S TCT       7 | Tyr Y TAT      62 | Cys C TGT       0
      TTC      53 |       TCC      22 |       TAC      28 |       TGC       8
Leu L TTA      37 |       TCA      17 | *** * TAA       0 | *** * TGA       0
      TTG       7 |       TCG      33 |       TAG       0 | Trp W TGG      48
------------------------------------------------------------------------------
Leu L CTT       8 | Pro P CCT      18 | His H CAT      16 | Arg R CGT      34
      CTC       5 |       CCC       6 |       CAC      24 |       CGC      55
      CTA      26 |       CCA       1 | Gln Q CAA      27 |       CGA      11
      CTG      36 |       CCG      39 |       CAG      61 |       CGG      22
------------------------------------------------------------------------------
Ile I ATT      65 | Thr T ACT       0 | Asn N AAT      49 | Ser S AGT      23
      ATC      28 |       ACC      23 |       AAC      11 |       AGC       6
      ATA       4 |       ACA      13 | Lys K AAA      61 | Arg R AGA       7
Met M ATG      28 |       ACG      33 |       AAG      26 |       AGG       2
------------------------------------------------------------------------------
Val V GTT      42 | Ala A GCT      31 | Asp D GAT      39 | Gly G GGT      16
      GTC       7 |       GCC      26 |       GAC      45 |       GGC      41
      GTA      25 |       GCA      29 | Glu E GAA      52 |       GGA      31
      GTG      48 |       GCG      25 |       GAG      16 |       GGG      21
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.22672    C:0.23836    A:0.23223    G:0.30270
position  2:    T:0.28615    C:0.19792    A:0.31679    G:0.19914
position  3:    T:0.28064    C:0.23775    A:0.20895    G:0.27267

Codon frequencies under model, for use in evolver:
  0.01904481  0.01613403  0.01417965  0.01850423
  0.01317232  0.01115908  0.00980734  0.01279843
  0.02108387  0.01786144  0.00000000  0.00000000
  0.01325388  0.01122818  0.00000000  0.01287768
  0.02002278  0.01696253  0.01490779  0.01945445
  0.01384874  0.01173212  0.01031096  0.01345565
  0.02216655  0.01877865  0.01650392  0.02153737
  0.01393449  0.01180476  0.01037480  0.01353897
  0.01950806  0.01652648  0.01452456  0.01895434
  0.01349273  0.01143052  0.01004589  0.01310975
  0.02159672  0.01829591  0.01607965  0.02098371
  0.01357627  0.01150130  0.01010810  0.01319092
  0.02542739  0.02154111  0.01893175  0.02470565
  0.01758683  0.01489888  0.01309412  0.01708764
  0.02814981  0.02384744  0.02095870  0.02735080
  0.01769572  0.01499114  0.01317520  0.01719344



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               0.4853 (0.0449 0.0926)
Shig4337             0.4853 (0.0449 0.0926)-1.0000 (0.0000 0.0000)
CFT073               0.0916 (0.0113 0.1236) 0.3134 (0.0483 0.1541) 0.3134 (0.0483 0.1541)
O157                 0.1076 (0.0113 0.1053) 0.3837 (0.0518 0.1349) 0.3837 (0.0518 0.1349) 0.1658 (0.0195 0.1177)
EDL933               0.1076 (0.0113 0.1053) 0.3837 (0.0518 0.1349) 0.3837 (0.0518 0.1349) 0.1658 (0.0195 0.1177)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 62
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1531.450044     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.02899  0.16362  0.00000  0.00000  0.01388  0.07259  0.06051  0.00000  0.00000  1.94898  0.87430  0.00000  0.00000  3.19532
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.33962

((1: 0.028995, (2: 0.000004, 3: 0.000004): 0.163624): 0.000000, (4: 0.072594, (5: 0.000004, 6: 0.000004): 0.060512): 0.013875);

((K12: 0.028995, (S2457T: 0.000004, Shig4337: 0.000004): 0.163624): 0.000000, (CFT073: 0.072594, (O157: 0.000004, EDL933: 0.000004): 0.060512): 0.013875);

Detailed output identifying parameters

kappa (ts/tv) =  1.94898


dN/dS for site classes (K=3)

p:   0.87430  0.00000  0.12570
w:   0.00000  1.00000  3.19532

dN & dS for each branch

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

   7..8       0.000    215.3    600.7   0.4017   0.0000   0.0000    0.0    0.0
   8..1       0.029    215.3    600.7   0.4017   0.0069   0.0173    3.7    4.2
   8..9       0.164    215.3    600.7   0.4017   0.0392   0.0975   21.0   23.5
   9..2       0.000    215.3    600.7   0.4017   0.0000   0.0000    0.0    0.0
   9..3       0.000    215.3    600.7   0.4017   0.0000   0.0000    0.0    0.0
   7..10      0.014    215.3    600.7   0.4017   0.0033   0.0083    1.8    2.0
  10..4       0.073    215.3    600.7   0.4017   0.0174   0.0432    9.3   10.4
  10..11      0.061    215.3    600.7   0.4017   0.0145   0.0360    7.8    8.7
  11..5       0.000    215.3    600.7   0.4017   0.0000   0.0000    0.0    0.0
  11..6       0.000    215.3    600.7   0.4017   0.0000   0.0000    0.0    0.0


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

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

    11 L      1.000**       3.195
    13 S      1.000**       3.195
    40 V      1.000**       3.195
    43 T      1.000**       3.195
    60 R      1.000**       3.195
    70 I      1.000**       3.195
    91 G      1.000**       3.195
   137 S      1.000**       3.195
   139 S      1.000**       3.195
   187 S      1.000**       3.195
   193 I      1.000**       3.195
   248 P      1.000**       3.195
   258 V      1.000**       3.195
   259 E      1.000**       3.195
   260 E      1.000**       3.195
   261 L      1.000**       3.195
   262 Q      1.000**       3.195
   263 A      1.000**       3.195
   264 F      1.000**       3.195
   265 V      1.000**       3.195
   266 D      1.000**       3.195
   268 I      1.000**       3.195
   270 E      1.000**       3.195
   271 T      1.000**       3.195
   272 P      1.000**       3.195


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

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

    13 S      0.763         3.968 +- 2.184
   187 S      0.782         4.058 +- 2.166
   258 V      0.782         4.052 +- 2.161
   259 E      0.679         3.550 +- 2.184
   260 E      0.888         4.533 +- 1.979
   261 L      0.788         4.082 +- 2.153
   262 Q      0.649         3.399 +- 2.318
   263 A      0.983*        4.968 +- 1.721
   264 F      0.619         3.248 +- 2.302
   265 V      0.561         2.975 +- 2.337
   266 D      0.872         4.459 +- 2.009
   268 I      0.604         3.178 +- 2.314
   271 T      0.880         4.535 +- 2.055



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:   0.958  0.041  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.005  0.077  0.205  0.265  0.208  0.122  0.063  0.032  0.016  0.008

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 0.001 0.029
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.056 0.204
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.113 0.534 0.056

sum of density on p0-p1 =   1.000000
