
seed used = 140000385

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1548.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 181
# site patterns = 97
    3   11    1    5    4    3    7   12    3    2    4    4    1    2    3
    3    3    2    2    1    1    1    2    1    1    2    1    2    3    1
    1    3    1    6    1    2    1    1    5    2    2    3    1    1    1
    1    1    1    1    1    1    1    1    1    1    2    1    1    1    1
    1    1    1    1    1    1    1    1    4    3    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       
K12                   ATG GAA GTC AAC AAA AAG CAG CTG GCT GAC ATT TTC GGT GCG AGT ATC CGT ACC TGG GAA GGA CCC GTT CGA GGC GGT GGC AAT GAG GTG CTT TAT TCT GCC GTT ATA AGA AGG GAT CGC CGG GAA CGG CAG GCC AGC ACA CTC CAG CCA GGG ACT ATT GAG TAC CAT CGA CTT ACG GCG GCC GAC GCA GAG AAA AGA GAC TCC GTG GCA TGT ACT TCG CGG ATC GGT ATT GCC CTC GAC GGG ATC CCC CGG TTT CCG GAA CGA GTT CCG GGG TTG AAC CGC GCT GAC AGA 
CFT073                ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... .A. ... ... ... ... ..G ... .T. ... ... G.. ..T ..C ..C ..A ..A C.. ..A .TT ... ..C ..G ..C ..T ..G ACG ..G ..A ... .A. ..A ..G ... ... ... ... ... ..T ..A A.G ..A T.. ... ... ..T ..T ..T ..A ... ..T ..T ..G A.. ... ... ... .T. GAA CAG TCA G.T 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ..G ... ... ... ..G ..T ... ... ... ... ..A ... ... ... ... .CC ... .A. ... ... ... ... ... A.. ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..G ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. GAA CAG TCA G.T 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ..G ... ... ... ..G ..T ... ... ... ... ..A ... ... ... ... .CC ... .A. ... ... ... ... ... A.. ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..G ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. GAA CAG TCA G.T 

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

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

#1: K12            
position  1:    T:0.09392    C:0.25414    A:0.25414    G:0.39779
position  2:    T:0.26519    C:0.19337    A:0.34807    G:0.19337
position  3:    T:0.23757    C:0.24862    A:0.19890    G:0.31492

#2: CFT073         
position  1:    T:0.10497    C:0.25967    A:0.25414    G:0.38122
position  2:    T:0.28177    C:0.19890    A:0.34254    G:0.17680
position  3:    T:0.27072    C:0.20442    A:0.19890    G:0.32597

#3: O157           
position  1:    T:0.09945    C:0.24862    A:0.25414    G:0.39779
position  2:    T:0.26519    C:0.19337    A:0.35912    G:0.18232
position  3:    T:0.23204    C:0.23757    A:0.20442    G:0.32597

#4: EDL933         
position  1:    T:0.09945    C:0.24862    A:0.25414    G:0.39779
position  2:    T:0.26519    C:0.19337    A:0.35912    G:0.18232
position  3:    T:0.23204    C:0.23757    A:0.20442    G:0.32597

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       5 | Ser S TCT       4 | Tyr Y TAT      12 | Cys C TGT       4
      TTC      16 |       TCC       2 |       TAC       3 |       TGC       0
Leu L TTA       0 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG       4 |       TCG       9 |       TAG       0 | Trp W TGG       8
------------------------------------------------------------------------------
Leu L CTT       9 | Pro P CCT       2 | His H CAT       8 | Arg R CGT      13
      CTC       7 |       CCC       8 |       CAC       1 |       CGC      10
      CTA       0 |       CCA       3 | Gln Q CAA       0 |       CGA       9
      CTG      50 |       CCG       7 |       CAG      37 |       CGG      19
------------------------------------------------------------------------------
Ile I ATT      24 | Thr T ACT       7 | Asn N AAT       8 | Ser S AGT      12
      ATC      21 |       ACC       9 |       AAC      21 |       AGC       4
      ATA      10 |       ACA       4 | Lys K AAA      22 | Arg R AGA       5
Met M ATG      12 |       ACG       4 |       AAG      14 |       AGG       7
------------------------------------------------------------------------------
Val V GTT      12 | Ala A GCT      14 | Asp D GAT      23 | Gly G GGT      19
      GTC       5 |       GCC      34 |       GAC      19 |       GGC       8
      GTA       2 |       GCA      16 | Glu E GAA      65 |       GGA       5
      GTG      18 |       GCG      13 |       GAG      22 |       GGG      10
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.09945    C:0.25276    A:0.25414    G:0.39365
position  2:    T:0.26934    C:0.19475    A:0.35221    G:0.18370
position  3:    T:0.24309    C:0.23204    A:0.20166    G:0.32320

Codon frequencies under model, for use in evolver:
  0.00665818  0.00635553  0.00552326  0.00885235
  0.00481438  0.00459554  0.00399374  0.00640093
  0.00870685  0.00831108  0.00000000  0.00000000
  0.00454122  0.00433480  0.00000000  0.00603776
  0.01692287  0.01615365  0.01403829  0.02249973
  0.01223654  0.01168033  0.01015076  0.01626903
  0.02212991  0.02112400  0.01835776  0.02942272
  0.01154227  0.01101762  0.00957483  0.01534597
  0.01701535  0.01624192  0.01411500  0.02262267
  0.01230340  0.01174416  0.01020623  0.01635793
  0.02225084  0.02123943  0.01845808  0.02958350
  0.01160534  0.01107782  0.00962716  0.01542982
  0.02635529  0.02515732  0.02186291  0.03504056
  0.01905690  0.01819068  0.01580857  0.02533702
  0.03446461  0.03289804  0.02858996  0.04582227
  0.01797566  0.01715858  0.01491163  0.02389946



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                 
CFT073               0.2073 (0.0630 0.3037)
O157                 0.3208 (0.0317 0.0988) 0.1274 (0.0400 0.3142)
EDL933               0.3208 (0.0317 0.0988) 0.1274 (0.0400 0.3142)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: 56
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):  -1026.229947     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
  1.02987  0.00000  8.07066  1.53283  0.00000  0.00000  1.47561  0.97390  0.00000  0.11915 513.97930
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  10.63336

(1: 1.029868, (2: 8.070661, (3: 0.000004, 4: 0.000004): 1.532828): 0.000000);

(K12: 1.029868, (CFT073: 8.070661, (O157: 0.000004, EDL933: 0.000004): 1.532828): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  1.47561


dN/dS for site classes (K=3)

p:   0.97390  0.00000  0.02610
w:   0.11915  1.00000513.97930

dN & dS for each branch

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

   5..1       1.030    138.1    404.9  13.5332   0.4491   0.0332    4.6  181.8
   5..6       0.000    138.1    404.9  13.5332   0.0000   0.0000    0.0    0.0
   6..2       8.071    138.1    404.9  13.5332   3.5194   0.2601   35.9 1424.9
   6..7       1.533    138.1    404.9  13.5332   0.6684   0.0494    6.8  270.6
   7..3       0.000    138.1    404.9  13.5332   0.0000   0.0000    0.0    0.0
   7..4       0.000    138.1    404.9  13.5332   0.0000   0.0000    0.0    0.0


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

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

    95 D      0.782         401.944
   178 R      1.000**       513.792
   179 A      0.999**       513.600
   180 D      0.999**       513.311
   181 R      0.597         306.910


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

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

    95 D      0.716         6.311 +- 3.757
   178 R      0.976*        8.371 +- 2.190
   179 A      0.967*        8.311 +- 2.287
   180 D      0.968*        8.310 +- 2.284
   181 R      0.547         4.919 +- 4.224



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:   0.748  0.251  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.002  0.007  0.017  0.034  0.058  0.088  0.126  0.170  0.221  0.277

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 0.012
 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 0.012 0.317
 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 0.141 0.515

sum of density on p0-p1 =   1.000000
