
seed used = 141368745

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b0599.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 2  	ls = 362
# site patterns = 79
    3    2    5    9    8    6   17    7    6    9    5    3    4   11    2
    8    6    4    2    4   21   12    2    8   11    2    1   17    4    1
   16   11    7    7    2    4    3    2    5    1   10    3    5    1    3
    7    3    5    3    2    1    6    5    3    1    1    7    2    5    1
    7    2    1    1    1    3    1    2    1    2    1    1    1    1    1
    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------
Phe TTT 11 11 | Ser TCT  1  1 | Tyr TAT  5  5 | Cys TGT  0  0
    TTC  4  4 |     TCC  3  3 |     TAC  4  4 |     TGC  3  3
Leu TTA  3  3 |     TCA  2  2 | *** TAA  0  0 | *** TGA  0  0
    TTG  5  6 |     TCG  1  1 |     TAG  0  0 | Trp TGG  4  4
--------------------------------------------------------------
Leu CTT  2  4 | Pro CCT  2  2 | His CAT  8  8 | Arg CGT  6  6
    CTC  6  6 |     CCC  0  0 |     CAC  5  5 |     CGC  7  7
    CTA  1  2 |     CCA  6  9 | Gln CAA 14 11 |     CGA  1  1
    CTG 25 21 |     CCG 12  9 |     CAG  7 10 |     CGG  0  0
--------------------------------------------------------------
Ile ATT 11 11 | Thr ACT  3  3 | Asn AAT 10  9 | Ser AGT  2  2
    ATC  8  8 |     ACC  8  8 |     AAC  3  4 |     AGC  6  5
    ATA  0  0 |     ACA  3  2 | Lys AAA  9  7 | Arg AGA  0  0
Met ATG  3  3 |     ACG  7  8 |     AAG  2  2 |     AGG  0  0
--------------------------------------------------------------
Val GTT  3  1 | Ala GCT  7  7 | Asp GAT 12 15 | Gly GGT 12 10
    GTC  7  9 |     GCC 16 19 |     GAC  8  5 |     GGC  6  8
    GTA  1  4 |     GCA  5  3 | Glu GAA  8  9 |     GGA  5  4
    GTG 20 17 |     GCG 18 19 |     GAG  7  7 |     GGG  4  5
--------------------------------------------------------------

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

#1: K12            
position  1:    T:0.12707    C:0.28177    A:0.20718    G:0.38398
position  2:    T:0.30387    C:0.25967    A:0.28177    G:0.15470
position  3:    T:0.26243    C:0.25967    A:0.16022    G:0.31768

#2: O157           
position  1:    T:0.12983    C:0.27901    A:0.19890    G:0.39227
position  2:    T:0.30387    C:0.26519    A:0.27901    G:0.15193
position  3:    T:0.26243    C:0.27072    A:0.15746    G:0.30939

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      22 | Ser S TCT       2 | Tyr Y TAT      10 | Cys C TGT       0
      TTC       8 |       TCC       6 |       TAC       8 |       TGC       6
Leu L TTA       6 |       TCA       4 | *** * TAA       0 | *** * TGA       0
      TTG      11 |       TCG       2 |       TAG       0 | Trp W TGG       8
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       4 | His H CAT      16 | Arg R CGT      12
      CTC      12 |       CCC       0 |       CAC      10 |       CGC      14
      CTA       3 |       CCA      15 | Gln Q CAA      25 |       CGA       2
      CTG      46 |       CCG      21 |       CAG      17 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      22 | Thr T ACT       6 | Asn N AAT      19 | Ser S AGT       4
      ATC      16 |       ACC      16 |       AAC       7 |       AGC      11
      ATA       0 |       ACA       5 | Lys K AAA      16 | Arg R AGA       0
Met M ATG       6 |       ACG      15 |       AAG       4 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       4 | Ala A GCT      14 | Asp D GAT      27 | Gly G GGT      22
      GTC      16 |       GCC      35 |       GAC      13 |       GGC      14
      GTA       5 |       GCA       8 | Glu E GAA      17 |       GGA       9
      GTG      37 |       GCG      37 |       GAG      14 |       GGG       9
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12845    C:0.28039    A:0.20304    G:0.38812
position  2:    T:0.30387    C:0.26243    A:0.28039    G:0.15331
position  3:    T:0.26243    C:0.26519    A:0.15884    G:0.31354

Codon frequencies under model, for use in evolver:
  0.01045394  0.01056399  0.00632739  0.01248971
  0.00902841  0.00912344  0.00546456  0.01078657
  0.00964614  0.00974768  0.00000000  0.00000000
  0.00527449  0.00533001  0.00000000  0.00630163
  0.02281882  0.02305902  0.01381139  0.02726249
  0.01970717  0.01991461  0.01192802  0.02354488
  0.02105555  0.02127719  0.01274415  0.02515584
  0.01151313  0.01163432  0.00696848  0.01375517
  0.01652398  0.01669791  0.01000135  0.01974180
  0.01427071  0.01442092  0.00863753  0.01704974
  0.01524712  0.01540762  0.00922852  0.01821630
  0.00833710  0.00842486  0.00504614  0.00996064
  0.03158665  0.03191914  0.01911823  0.03773773
  0.02727938  0.02756653  0.01651120  0.03259168
  0.02914586  0.02945266  0.01764092  0.03482163
  0.01593690  0.01610466  0.00964602  0.01904040



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                 
O157                 0.0618 (0.0075 0.1207)


TREE #  1:  (1, 2);   MP score: 35
lnL(ntime:  2  np:  7):  -1599.010349     +0.000000
   3..1     3..2  
  0.13404  0.00886 10.15829  0.98780  0.00000  0.00595 20.93415
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.14291

(1: 0.134044, 2: 0.008863);

(K12: 0.134044, O157: 0.008863);

Detailed output identifying parameters

kappa (ts/tv) = 10.15829


dN/dS for site classes (K=3)

p:   0.98780  0.00000  0.01220
w:   0.00595  1.00000 20.93415

dN & dS for each branch

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

   3..1       0.134    364.1    721.9   0.2613   0.0229   0.0878   32.0   16.6
   3..2       0.009    364.1    721.9   0.2613   0.0015   0.0058    2.1    1.1


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

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

    43 K      1.000**       20.933
   116 V      0.760         15.903
   218 S      1.000**       20.933
   355 K      0.851         17.806


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

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

    43 K      0.917         5.761 +- 2.952
   218 S      0.917         5.761 +- 2.951
   355 K      0.533         3.552 +- 3.528



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:   0.994  0.006  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.076  0.099  0.110  0.113  0.111  0.107  0.102  0.098  0.094  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 0.000
 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 0.013
 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 0.012 0.974

sum of density on p0-p1 =   1.000000
