
seed used = 140010557

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2542.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 480
# site patterns = 91
    6    9   16    6    8   15    5    1   11    3    7   11    9    8   14
    2    4   13   16    2    6   12   80    7   20    6    7    4   18    1
   10    2    2    1    1    2    2    1    1    1   12    6    4    1   10
   10    9    2    2    1    1    1    2    2    3    1    5    2    1    9
    2    4    1    2    1    2    1    3    2    1    5    1    1    2    1
    1    1    2    1    1    1    1    1    1    1    1    1    1    1    1
    1

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



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT  7  7  7 | Ser TCT  0  1  1 | Tyr TAT  2  2  2 | Cys TGT  2  2  2
    TTC  2  2  2 |     TCC  4  4  4 |     TAC  2  2  2 |     TGC  4  4  4
Leu TTA  7  6  6 |     TCA  2  3  3 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  2  4  4 |     TCG  2  2  2 |     TAG  0  0  0 | Trp TGG 10 10 10
--------------------------------------------------------------------------
Leu CTT 10 11 11 | Pro CCT  2  2  2 | His CAT  6  8  8 | Arg CGT  5  5  5
    CTC  2  2  2 |     CCC  4  4  4 |     CAC  3  3  3 |     CGC 13 14 14
    CTA  6  4  4 |     CCA  3  2  2 | Gln CAA  7  8  8 |     CGA  5  3  3
    CTG 22 21 21 |     CCG 10 10 10 |     CAG 18 17 17 |     CGG  1  1  1
--------------------------------------------------------------------------
Ile ATT 16 15 15 | Thr ACT  4  3  3 | Asn AAT  9  9  9 | Ser AGT  2  3  3
    ATC  9  9  9 |     ACC  7  8  8 |     AAC 11 10 10 |     AGC  6  5  5
    ATA  2  1  1 |     ACA  2  4  4 | Lys AAA  9 10 10 | Arg AGA  2  2  2
Met ATG  6  6  6 |     ACG  7  6  6 |     AAG  2  1  1 |     AGG  0  0  0
--------------------------------------------------------------------------
Val GTT  2  2  2 | Ala GCT  9  8  8 | Asp GAT 18 18 18 | Gly GGT 14 12 12
    GTC  6  6  6 |     GCC 15 16 16 |     GAC  2  3  3 |     GGC 11 13 13
    GTA  2  3  3 |     GCA  9  9  9 | Glu GAA 17 16 16 |     GGA  2  3  3
    GTG 12 12 12 |     GCG 11 11 11 |     GAG  8  8  8 |     GGG  5  4  4
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.11500    C:0.29250    A:0.23500    G:0.35750
position  2:    T:0.28250    C:0.22750    A:0.28500    G:0.20500
position  3:    T:0.27000    C:0.25250    A:0.18750    G:0.29000

#2: O157           
position  1:    T:0.12250    C:0.28750    A:0.23000    G:0.36000
position  2:    T:0.27750    C:0.23250    A:0.28750    G:0.20250
position  3:    T:0.27000    C:0.26250    A:0.18500    G:0.28250

#3: EDL933         
position  1:    T:0.12250    C:0.28750    A:0.23000    G:0.36000
position  2:    T:0.27750    C:0.23250    A:0.28750    G:0.20250
position  3:    T:0.27000    C:0.26250    A:0.18500    G:0.28250

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      21 | Ser S TCT       2 | Tyr Y TAT       6 | Cys C TGT       6
      TTC       6 |       TCC      12 |       TAC       6 |       TGC      12
Leu L TTA      19 |       TCA       8 | *** * TAA       0 | *** * TGA       0
      TTG      10 |       TCG       6 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT      32 | Pro P CCT       6 | His H CAT      22 | Arg R CGT      15
      CTC       6 |       CCC      12 |       CAC       9 |       CGC      41
      CTA      14 |       CCA       7 | Gln Q CAA      23 |       CGA      11
      CTG      64 |       CCG      30 |       CAG      52 |       CGG       3
------------------------------------------------------------------------------
Ile I ATT      46 | Thr T ACT      10 | Asn N AAT      27 | Ser S AGT       8
      ATC      27 |       ACC      23 |       AAC      31 |       AGC      16
      ATA       4 |       ACA      10 | Lys K AAA      29 | Arg R AGA       6
Met M ATG      18 |       ACG      19 |       AAG       4 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       6 | Ala A GCT      25 | Asp D GAT      54 | Gly G GGT      38
      GTC      18 |       GCC      47 |       GAC       8 |       GGC      37
      GTA       8 |       GCA      27 | Glu E GAA      49 |       GGA       8
      GTG      36 |       GCG      33 |       GAG      24 |       GGG      13
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.12000    C:0.28917    A:0.23167    G:0.35917
position  2:    T:0.27917    C:0.23083    A:0.28667    G:0.20333
position  3:    T:0.27000    C:0.25917    A:0.18583    G:0.28500

Codon frequencies under model, for use in evolver:
  0.00923648  0.00886588  0.00635721  0.00974962
  0.00763733  0.00733089  0.00525656  0.00806163
  0.00948463  0.00910407  0.00000000  0.00000000
  0.00672747  0.00645754  0.00000000  0.00710122
  0.02225735  0.02136431  0.01531911  0.02349387
  0.01840384  0.01766542  0.01266684  0.01942628
  0.02285531  0.02193828  0.01573066  0.02412505
  0.01621133  0.01556087  0.01115780  0.01711196
  0.01783154  0.01711608  0.01227294  0.01882218
  0.01474429  0.01415270  0.01014808  0.01556342
  0.01831060  0.01757591  0.01260266  0.01932785
  0.01298775  0.01246664  0.00893910  0.01370929
  0.02764530  0.02653608  0.01902748  0.02918115
  0.02285895  0.02194177  0.01573317  0.02412889
  0.02838801  0.02724899  0.01953866  0.02996512
  0.02013568  0.01932777  0.01385882  0.02125433



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                 
O157                 0.1964 (0.0140 0.0714)
EDL933               0.1964 (0.0140 0.0714)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1787.013510     +0.000000
   4..1     4..5     5..2     5..3  
  0.17892  0.03146  0.00000  0.00000  3.67211  0.99692  0.00000  0.20897 354.53350
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.21039

(1: 0.178921, (2: 0.000004, 3: 0.000004): 0.031465);

(K12: 0.178921, (O157: 0.000004, EDL933: 0.000004): 0.031465);

Detailed output identifying parameters

kappa (ts/tv) =  3.67211


dN/dS for site classes (K=3)

p:   0.99692  0.00000  0.00308
w:   0.20897  1.00000354.53350

dN & dS for each branch

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

   4..1       0.179    440.1    999.9   1.2998   0.0642   0.0494   21.7   64.2
   4..5       0.031    440.1    999.9   1.2998   0.0113   0.0087    3.8   11.3
   5..2       0.000    440.1    999.9   1.2998   0.0000   0.0000    0.0    0.0
   5..3       0.000    440.1    999.9   1.2998   0.0000   0.0000    0.0    0.0


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

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

    63 Q      0.999**       354.128


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

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

    63 Q      0.933         6.017 +- 2.878
   439 P      0.505         3.556 +- 3.543
   469 L      0.503         3.544 +- 3.541



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:   0.657  0.280  0.055  0.007  0.001  0.000  0.000  0.000  0.000  0.000
w2:   0.076  0.082  0.096  0.108  0.114  0.116  0.113  0.107  0.099  0.090

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008
 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 0.004 0.058
 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 0.005 0.027 0.249
 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 0.006 0.021 0.105 0.510

sum of density on p0-p1 =   1.000000
