
seed used = 139999773

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1471.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 318
# site patterns = 158
    2    1    1    1    1    8    1    1    3    3    1    1    1    6    1
    1    1    1    1    1    1    2    2    6    1    2    1    1    1    1
    1    1    1    1    1   12    2    1    1    2    2    1    1    1    1
    1    1    2    2    1    1    1    1    1    1    1    2    1    1    1
    1    1    1    1   10    1    1    1    1    1    2    1    1    1    2
    1    1    1    1    1    1    1    1    7   10    4    1    8   19    1
    5    7    2    1    8    4    1    5    2    1    4    4    2    1    2
    3    4    2    1    1    5    4    1    2    1    1    1    1    1    1
    1    3    1    3    1    4    1    1    3    2    1    1    2    1    1
    1    2    1    1    2    1    1    1    2    2    2    1    1    1    1
    1    1    1    1    1    1    1    1

K12                                  ATG ATC ACT GAC CTT ATA TTA CAC AAT CAT CCC AGG ATG AAA ACA ATC ACT TTA AAC GAC AAC ATT GCA CAT TTA AAC GCC AAA AAC ACT ACA AAA CTG GAA TAT TTA AAC TTA AGC AAT AAT TTA CTG CCA ACC AAT GAC ATT GAT CAA CTA ATA TCA TCA AAA CTT TGG CAT GTA TTA GTT AAC GGC ATC AAC AAT GAT CCA CTT GCA CAA ATG CAG TAC ACT GTA AGA ATA GAT GAC GAA GTG ACC ATT GAT TCA GGA CTT AAT ACC ACT CAA CCA GGG CTG TTC ACA TCT ATC TTC ACA TTT GCA ACC TAC AGA CTC GTA AAG CTA AGT AAT GCT GAG TTT CCT GGC AGT GCT AGG GTT TAT GCG CTA GTG GAA TGC TGG AGC GTT GCA GGT TCC ACA CAC GAC CCC TTG ACG TTG ATA TTC TGC CAG GCT AAA TAT CCA AGA GAC ACC CAC AAT GGA ACT AAA CAG ACT 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC 
O157                                 ... .AA TTC CCT TCA ... ..T A.. --- --- --- .AA ..A ... C.. CAA T.C A.. C.G C.A --- --- --- ... CC. G.A AAA ..T C.A CT. .AC TGG A.. CTC G.A ... ..T AA. T.G ..A G.A CGT A.A .TT ..A GG. ..A ..C C.. .GT .CG GA. .GT CG. --- --- --- A.C .A. GCC .C. ..A A.G ..A ... TG. .C. TTT T.G T.G A.. CA. A.T --- --- --- --- --- --- --- --- --- GA. ... ... ... ... ... ... T.T ... ... ... ... ... ... ..C ... ... C.. ... ... ... ... ... ... ... ... ..A ..T ... ..C A.. ... A.. .A. ... ..C TG. ... A.. ... ... ... ... ... ... ... ... ... A.. ..A ... G.. ... .C. ... ..A ... ... ..G ..T ... ... ... G.. A.A T.. ..G ... ..T .G. G.G A.. .G. ..G A.. .GC 
EDL933                               ... .AA TTC CCT TCA ... ..T A.. --- --- --- .AA ..A ... C.. CAA T.C A.. C.G C.A --- --- --- ... CC. G.A AAA ..T C.A CT. .AC TGG A.. CTC G.A ... ..T AA. T.G ..A G.A CGT A.A .TT ..A GG. ..A ..C C.. .GT .CG GA. .GT CG. --- --- --- A.C .A. GCC .C. ..A A.G ..A ... TG. .C. TTT T.G T.G A.. CA. A.T --- --- --- --- --- --- --- --- --- GA. ... ... ... ... ... ... T.T ... ... ... ... ... ... ..C ... ... C.. ... ... ... ... ... ... ... ... ..A ..T ... ..C A.. ... A.. .A. ... ..C TG. ... A.. ... ... ... ... ... ... ... ... ... A.. ..A ... G.. ... .C. ... ..A ... ... ..G ..T ... ... ... G.. A.A T.. ..G ... ..T .G. G.G A.. .G. ..G A.. .GC 



Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  5  5  5  7  7 | Ser TCT  5  5  5  6  6 | Tyr TAT  5  5  5  3  3 | Cys TGT  0  0  0  3  3
    TTC  6  5  5  5  5 |     TCC  2  2  2  3  3 |     TAC  3  3  3  2  2 |     TGC  2  1  1  2  2
Leu TTA 18 18 18 13 13 |     TCA  6  6  6  6  6 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  3  3  3  3  3 |     TCG  0  0  0  1  1 |     TAG  0  0  0  0  0 | Trp TGG  3  3  3  3  3
--------------------------------------------------------------------------------------------------
Leu CTT 11 11 11 11 11 | Pro CCT  1  1  1  1  1 | His CAT 10 10 10  9  9 | Arg CGT  0  0  0  2  2
    CTC  4  5  5  6  6 |     CCC  3  3  3  2  2 |     CAC  3  3  3  1  1 |     CGC  0  1  1  1  1
    CTA  5  5  5  3  3 |     CCA  5  5  5  4  4 | Gln CAA 10 10 10 10 10 |     CGA  0  0  0  1  1
    CTG 10 10 10  8  8 |     CCG  0  0  0  1  1 |     CAG  4  4  4  4  4 |     CGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Ile ATT 11 11 11  9  9 | Thr ACT 12 11 11  7  7 | Asn AAT 33 33 33 23 23 | Ser AGT  6  6  6  6  6
    ATC  5  5  5  4  4 |     ACC  5  6  6  2  2 |     AAC 18 19 19 17 17 |     AGC  4  4  4  5  5
    ATA 11 11 11 12 12 |     ACA  8  7  7  6  6 | Lys AAA 12 12 12 17 17 | Arg AGA  5  5  5  4  4
Met ATG  4  4  4  4  4 |     ACG  1  1  1  1  1 |     AAG  1  1  1  2  2 |     AGG  2  2  2  3  3
--------------------------------------------------------------------------------------------------
Val GTT  4  4  4  2  2 | Ala GCT  4  4  4  4  4 | Asp GAT 14 14 14 10 10 | Gly GGT  1  1  1  1  1
    GTC  0  1  1  0  0 |     GCC  1  1  1  2  2 |     GAC  6  5  5  2  2 |     GGC  2  2  2  1  1
    GTA  4  4  4  2  2 |     GCA  6  6  6  3  3 | Glu GAA  6  6  6 14 14 |     GGA  2  2  2  2  2
    GTG  2  2  2  1  1 |     GCG  1  1  1  1  1 |     GAG  2  2  2  3  3 |     GGG  1  1  1  1  1
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.18239    C:0.20755    A:0.43396    G:0.17610
position  2:    T:0.32390    C:0.18868    A:0.39937    G:0.08805
position  3:    T:0.38365    C:0.20126    A:0.30818    G:0.10692

#2: S2457T         
position  1:    T:0.17610    C:0.21384    A:0.43396    G:0.17610
position  2:    T:0.32704    C:0.18553    A:0.39937    G:0.08805
position  3:    T:0.38050    C:0.20755    A:0.30503    G:0.10692

#3: Shig4337       
position  1:    T:0.17610    C:0.21384    A:0.43396    G:0.17610
position  2:    T:0.32704    C:0.18553    A:0.39937    G:0.08805
position  3:    T:0.38050    C:0.20755    A:0.30503    G:0.10692

#4: O157           
position  1:    T:0.19521    C:0.21918    A:0.41781    G:0.16781
position  2:    T:0.30822    C:0.17123    A:0.40068    G:0.11986
position  3:    T:0.35616    C:0.18836    A:0.33219    G:0.12329

#5: EDL933         
position  1:    T:0.19521    C:0.21918    A:0.41781    G:0.16781
position  2:    T:0.30822    C:0.17123    A:0.40068    G:0.11986
position  3:    T:0.35616    C:0.18836    A:0.33219    G:0.12329

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      29 | Ser S TCT      27 | Tyr Y TAT      21 | Cys C TGT       6
      TTC      26 |       TCC      12 |       TAC      13 |       TGC       8
Leu L TTA      80 |       TCA      30 | *** * TAA       0 | *** * TGA       0
      TTG      15 |       TCG       2 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT      55 | Pro P CCT       5 | His H CAT      48 | Arg R CGT       4
      CTC      26 |       CCC      13 |       CAC      11 |       CGC       4
      CTA      21 |       CCA      23 | Gln Q CAA      50 |       CGA       2
      CTG      46 |       CCG       2 |       CAG      20 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      51 | Thr T ACT      48 | Asn N AAT     145 | Ser S AGT      30
      ATC      23 |       ACC      21 |       AAC      90 |       AGC      22
      ATA      57 |       ACA      34 | Lys K AAA      70 | Arg R AGA      23
Met M ATG      20 |       ACG       5 |       AAG       7 |       AGG      12
------------------------------------------------------------------------------
Val V GTT      16 | Ala A GCT      20 | Asp D GAT      62 | Gly G GGT       5
      GTC       2 |       GCC       7 |       GAC      20 |       GGC       8
      GTA      16 |       GCA      24 | Glu E GAA      46 |       GGA      10
      GTG       8 |       GCG       5 |       GAG      12 |       GGG       5
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.18466    C:0.21456    A:0.42783    G:0.17295
position  2:    T:0.31925    C:0.18075    A:0.39987    G:0.10013
position  3:    T:0.37191    C:0.19896    A:0.31599    G:0.11313

Codon frequencies under model, for use in evolver:
  0.02277923  0.01218609  0.01935438  0.00692935
  0.01289741  0.00689966  0.01095829  0.00392334
  0.02853203  0.01526364  0.00000000  0.00000000
  0.00714461  0.00382211  0.00000000  0.00217336
  0.02646882  0.01415990  0.02248925  0.00805171
  0.01498642  0.00801721  0.01273322  0.00455881
  0.03315342  0.01773592  0.02816881  0.01008513
  0.00830183  0.00444119  0.00705365  0.00252538
  0.05277723  0.02823397  0.04484219  0.01605461
  0.02988202  0.01598583  0.02538927  0.00908998
  0.06610590  0.03536435  0.05616690  0.02010914
  0.01655335  0.00885546  0.01406456  0.00503546
  0.02133548  0.01141373  0.01812770  0.00649016
  0.01207996  0.00646236  0.01026375  0.00367467
  0.02672366  0.01429622  0.02270577  0.00812923
  0.00669178  0.00357987  0.00568567  0.00203561



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               0.5518 (0.0054 0.0097)
Shig4337             0.5518 (0.0054 0.0097)-1.0000 (0.0000 0.0000)
O157                 0.7473 (0.1928 0.2580) 0.7972 (0.1930 0.2421) 0.7972 (0.1930 0.2421)
EDL933               0.7473 (0.1928 0.2580) 0.7972 (0.1930 0.2421) 0.7972 (0.1930 0.2421)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  8  np: 13):  -1803.260344     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.51713  0.01862  0.00159  0.00000  0.00000  0.86051  0.00000  0.00000  2.57483  0.53108  0.23590  0.00000 13.01614
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.39787

((1: 0.018618, (2: 0.000004, 3: 0.000004): 0.001591): 0.517135, (4: 0.000004, 5: 0.000004): 0.860513);

((K12: 0.018618, (S2457T: 0.000004, Shig4337: 0.000004): 0.001591): 0.517135, (O157: 0.000004, EDL933: 0.000004): 0.860513);

Detailed output identifying parameters

kappa (ts/tv) =  2.57483


dN/dS for site classes (K=3)

p:   0.53108  0.23590  0.23302
w:   0.00000  1.00000 13.01614

dN & dS for each branch

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

   6..7       0.517    235.8    718.2   3.2690   0.2081   0.0637   15.0  149.4
   7..1       0.019    235.8    718.2   3.2690   0.0075   0.0023    0.5    5.4
   7..8       0.002    235.8    718.2   3.2690   0.0006   0.0002    0.0    0.5
   8..2       0.000    235.8    718.2   3.2690   0.0000   0.0000    0.0    0.0
   8..3       0.000    235.8    718.2   3.2690   0.0000   0.0000    0.0    0.0
   6..9       0.861    235.8    718.2   3.2690   0.3463   0.1059   25.0  248.7
   9..4       0.000    235.8    718.2   3.2690   0.0000   0.0000    0.0    0.0
   9..5       0.000    235.8    718.2   3.2690   0.0000   0.0000    0.0    0.0


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

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

     2 I      0.885         11.638
     3 T      0.950*        12.416
     4 D      0.984*        12.826
     5 L      0.977*        12.743
     8 H      0.631         8.582
    12 R      0.772         10.277
    15 T      0.630         8.574
    16 I      0.990*        12.891
    17 T      0.728         9.748
    18 L      0.611         8.338
    19 N      0.944         12.340
    20 D      0.943         12.327
    26 L      0.892         11.718
    27 N      0.844         11.138
    28 A      0.991**       12.903
    30 N      0.911         11.950
    31 T      0.902         11.841
    32 T      0.901         11.822
    33 K      0.993**       12.931
    34 L      0.648         8.783
    35 E      0.994**       12.950
    36 Y      0.951*        12.427
    39 L      0.950         12.412
    40 S      0.970*        12.659
    42 N      0.844         11.138
    43 N      0.813         10.771
    44 L      0.992**       12.925
    45 L      0.871         11.464
    46 P      0.752         10.030
    48 N      0.841         11.109
    51 D      0.531         7.383
    52 Q      0.876         11.531
    53 L      0.746         9.967
    54 I      0.876         11.528
    55 S      0.938         12.271
    56 S      0.971*        12.663
    61 H      0.735         9.834
    62 V      0.566         7.799
    63 L      0.994**       12.943
    66 G      0.955*        12.477
    69 N      0.913         11.965
    70 D      0.556         7.676
    71 P      0.977*        12.738
    72 L      0.845         11.081
    73 A      0.829         10.959
    74 Q      0.530         7.371
    75 M      0.957*        12.502
    76 Q      0.932         12.201
    92 T      0.944         12.347
   101 T      0.729         9.755
   120 F      0.699         9.395
   146 F      0.586         8.038
   147 P      0.578         7.947
   163 A      0.979*        12.759
   184 Q      0.530         7.371
   215 N      0.813         10.771
   233 D      0.959*        12.521
   259 C      0.882         11.595
   273 Y      0.914         11.981
   277 D      0.531         7.383
   283 P      0.563         7.770
   297 H      0.610         8.333
   301 N      0.882         11.602
   308 T      0.546         7.560
   315 Q      0.632         8.589
   318 T      0.924         12.101


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

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

     2 I      0.913         8.694 +- 2.686
     3 T      0.968*        9.193 +- 1.853
     4 D      0.988*        9.363 +- 1.443
     5 L      0.983*        9.319 +- 1.564
     7 L      0.609         5.952 +- 4.367
     8 H      0.717         6.926 +- 4.074
    12 R      0.800         7.675 +- 3.672
    15 T      0.708         6.848 +- 4.110
    16 I      0.993**       9.404 +- 1.318
    17 T      0.762         7.338 +- 3.878
    18 L      0.699         6.762 +- 4.143
    19 N      0.967*        9.185 +- 1.868
    20 D      0.968*        9.190 +- 1.857
    26 L      0.920         8.758 +- 2.602
    27 N      0.919         8.757 +- 2.570
    28 A      0.994**       9.412 +- 1.295
    29 K      0.546         5.382 +- 4.463
    30 N      0.951*        9.039 +- 2.144
    31 T      0.948         9.015 +- 2.183
    32 T      0.936         8.903 +- 2.377
    33 K      0.993**       9.411 +- 1.298
    34 L      0.726         7.005 +- 4.040
    35 E      0.996**       9.431 +- 1.233
    36 Y      0.972*        9.226 +- 1.779
    39 L      0.969*        9.202 +- 1.832
    40 S      0.980*        9.297 +- 1.615
    41 N      0.544         5.364 +- 4.464
    42 N      0.919         8.757 +- 2.570
    43 N      0.900         8.594 +- 2.775
    44 L      0.993**       9.405 +- 1.320
    45 L      0.903         8.608 +- 2.794
    46 P      0.764         7.359 +- 3.873
    48 N      0.919         8.759 +- 2.567
    49 D      0.588         5.759 +- 4.408
    51 D      0.634         6.177 +- 4.325
    52 Q      0.927         8.830 +- 2.481
    53 L      0.797         7.656 +- 3.673
    54 I      0.935         8.900 +- 2.368
    55 S      0.932         8.863 +- 2.468
    56 S      0.981*        9.307 +- 1.591
    61 H      0.768         7.390 +- 3.853
    62 V      0.651         6.330 +- 4.292
    63 L      0.995**       9.425 +- 1.254
    64 V      0.557         5.482 +- 4.434
    65 N      0.571         5.606 +- 4.435
    66 G      0.969*        9.198 +- 1.848
    69 N      0.953*        9.054 +- 2.117
    70 D      0.639         6.225 +- 4.321
    71 P      0.984*        9.327 +- 1.540
    72 L      0.877         8.349 +- 3.146
    73 A      0.850         8.131 +- 3.305
    74 Q      0.627         6.111 +- 4.344
    75 M      0.973*        9.233 +- 1.765
    76 Q      0.961*        9.126 +- 1.986
    92 T      0.969*        9.194 +- 1.849
   101 T      0.759         7.315 +- 3.893
   120 F      0.767         7.384 +- 3.842
   140 A      0.551         5.427 +- 4.441
   146 F      0.670         6.503 +- 4.238
   147 P      0.667         6.479 +- 4.244
   163 A      0.986*        9.350 +- 1.477
   175 V      0.529         5.227 +- 4.456
   184 Q      0.627         6.111 +- 4.344
   211 A      0.601         5.873 +- 4.383
   215 N      0.900         8.594 +- 2.775
   228 T      0.597         5.839 +- 4.389
   233 D      0.975*        9.251 +- 1.725
   259 C      0.905         8.622 +- 2.784
   260 N      0.544         5.364 +- 4.464
   273 Y      0.951*        9.040 +- 2.143
   277 D      0.634         6.177 +- 4.325
   283 P      0.688         6.665 +- 4.169
   297 H      0.720         6.953 +- 4.056
   301 N      0.937         8.920 +- 2.337
   307 G      0.587         5.748 +- 4.399
   308 T      0.650         6.325 +- 4.284
   315 Q      0.731         7.048 +- 4.013
   318 T      0.956*        9.081 +- 2.070



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:   0.546  0.320  0.110  0.022  0.003  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.000  0.004  0.026  0.083  0.180  0.299  0.408

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 0.001 0.001 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.018 0.004 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 0.090 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 0.001 0.024 0.153 0.149 0.004 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.015 0.123 0.251 0.122 0.003 0.000 0.000 0.000

sum of density on p0-p1 =   1.000000
