
seed used = 141391809

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b0056.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 240
# site patterns = 111
    9    7    1    3    3    1    6    2    1    3    6    4   10    2    2
    6    6    2    2    5    2    3    3    1    4    4    1    1    3    4
    6    2    1    2    5    5    4    4    4    1    1    1    1    1    3
    2    1    3    1    1    1    1    1    2    1    3    1    1    1    1
    1    1    1    2    1    2    1    1    3    1    2    1    1    1    1
    1    1    1    1    1    4    4    4    2    3    1    1    1    1    1
    1    1    2    1    1    1    2    1    1    1    1    2    1    1    1
    1    1    1    1    1    1

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



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

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

#1: K12            
position  1:    T:0.16204    C:0.18519    A:0.37963    G:0.27315
position  2:    T:0.31944    C:0.16667    A:0.34259    G:0.17130
position  3:    T:0.26389    C:0.23611    A:0.17593    G:0.32407

#2: O157           
position  1:    T:0.14583    C:0.15000    A:0.37917    G:0.32500
position  2:    T:0.29583    C:0.18333    A:0.37917    G:0.14167
position  3:    T:0.34167    C:0.23333    A:0.18750    G:0.23750

#3: EDL933         
position  1:    T:0.14583    C:0.15000    A:0.37917    G:0.32500
position  2:    T:0.29583    C:0.18333    A:0.37917    G:0.14167
position  3:    T:0.34167    C:0.23333    A:0.18750    G:0.23750

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      14 | Ser S TCT       0 | Tyr Y TAT       9 | Cys C TGT       6
      TTC      16 |       TCC       0 |       TAC      11 |       TGC       3
Leu L TTA      12 |       TCA       9 | *** * TAA       0 | *** * TGA       0
      TTG      12 |       TCG       0 |       TAG       0 | Trp W TGG      13
------------------------------------------------------------------------------
Leu L CTT      19 | Pro P CCT       3 | His H CAT       8 | Arg R CGT       2
      CTC       4 |       CCC       7 |       CAC       4 |       CGC       5
      CTA       7 |       CCA       5 | Gln Q CAA       6 |       CGA       0
      CTG      19 |       CCG       7 |       CAG      13 |       CGG       3
------------------------------------------------------------------------------
Ile I ATT      14 | Thr T ACT      19 | Asn N AAT      38 | Ser S AGT       7
      ATC      16 |       ACC      15 |       AAC      19 |       AGC      10
      ATA       3 |       ACA       9 | Lys K AAA      41 | Arg R AGA       5
Met M ATG      31 |       ACG      10 |       AAG      24 |       AGG       3
------------------------------------------------------------------------------
Val V GTT      12 | Ala A GCT      28 | Asp D GAT      23 | Gly G GGT      19
      GTC      13 |       GCC       4 |       GAC      17 |       GGC      19
      GTA       5 |       GCA       8 | Glu E GAA      18 |       GGA       0
      GTG      14 |       GCG       0 |       GAG      25 |       GGG      10
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.15086    C:0.16092    A:0.37931    G:0.30891
position  2:    T:0.30316    C:0.17816    A:0.36782    G:0.15086
position  3:    T:0.31753    C:0.23420    A:0.18391    G:0.26437

Codon frequencies under model, for use in evolver:
  0.01495698  0.01103162  0.00866287  0.01245287
  0.00878989  0.00648304  0.00509097  0.00731828
  0.01814686  0.01338434  0.00000000  0.00000000
  0.00744305  0.00548967  0.00000000  0.00619693
  0.01595412  0.01176706  0.00924039  0.01328306
  0.00937588  0.00691524  0.00543037  0.00780616
  0.01935665  0.01427663  0.01121109  0.01611595
  0.00793925  0.00585565  0.00459830  0.00661006
  0.03760613  0.02773665  0.02178093  0.03131008
  0.02210029  0.01630021  0.01280017  0.01840024
  0.04562640  0.03365205  0.02642615  0.03798759
  0.01871395  0.01380260  0.01083885  0.01558085
  0.03062620  0.02258856  0.01773825  0.02549874
  0.01799834  0.01327479  0.01042438  0.01498504
  0.03715786  0.02740602  0.02152129  0.03093686
  0.01524053  0.01124075  0.00882709  0.01268895



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                 0.5769 (0.1370 0.2375)
EDL933               0.5769 (0.1370 0.2375)-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):  -1266.803140     +0.000000
   4..1     4..5     5..2     5..3  
  0.00000  9.89054  0.00000  0.00000  3.08234  0.87057  0.00000  0.54867 408.28339
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   9.89055

(1: 0.000004, (2: 0.000004, 3: 0.000004): 9.890541);

(K12: 0.000004, (O157: 0.000004, EDL933: 0.000004): 9.890541);

Detailed output identifying parameters

kappa (ts/tv) =  3.08234


dN/dS for site classes (K=3)

p:   0.87057  0.00000  0.12943
w:   0.54867  1.00000408.28339

dN & dS for each branch

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

   4..1       0.000    189.4    530.6  53.3206   0.0000   0.0000    0.0    0.0
   4..5       9.891    189.4    530.6  53.3206   4.4441   0.0833   15.8 2357.9
   5..2       0.000    189.4    530.6  53.3206   0.0000   0.0000    0.0    0.0
   5..3       0.000    189.4    530.6  53.3206   0.0000   0.0000    0.0    0.0


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

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

   172 K      1.000**       408.138
   178 S      0.927         378.496
   180 D      0.881         359.593
   184 E      0.983*        401.307
   185 R      0.824         336.663
   218 V      0.852         348.086
   219 L      0.955*        390.135
   220 P      0.997**       407.064
   221 R      0.999**       407.872
   222 T      0.846         345.488
   223 V      0.871         355.710
   224 L      0.999**       407.935
   226 R      0.996**       406.609
   227 T      0.846         345.488
   228 V      0.852         348.086
   229 L      1.000**       408.136
   231 R      0.998**       407.324
   232 T      0.994**       405.971
   234 L      0.999**       407.918
   236 W      0.999**       407.723
   237 T      0.999**       407.757
   238 V      0.998**       407.595
   239 L      0.999**       407.805
   240 P      0.970*        396.195


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

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

    10 V      0.688         7.246 +- 4.466
    17 K      0.653         6.907 +- 4.591
    31 V      0.646         6.839 +- 4.610
    65 N      0.690         7.261 +- 4.460
    66 Q      0.758         7.924 +- 4.129
    67 T      0.684         7.208 +- 4.481
    74 E      0.693         7.293 +- 4.446
    80 I      0.722         7.571 +- 4.321
    85 R      0.718         7.536 +- 4.337
    90 N      0.747         7.820 +- 4.190
    97 K      0.693         7.293 +- 4.446
   108 L      0.755         7.893 +- 4.148
   115 R      0.794         8.266 +- 3.904
   134 K      0.653         6.907 +- 4.591
   135 N      0.653         6.907 +- 4.591
   136 K      0.632         6.701 +- 4.649
   148 Q      0.844         8.747 +- 3.510
   157 K      0.632         6.701 +- 4.649
   172 K      0.998**       10.221 +- 0.704
   178 S      0.978*        10.034 +- 1.482
   180 D      0.956*        9.830 +- 1.994
   181 I      0.722         7.571 +- 4.321
   184 E      0.985*        10.100 +- 1.269
   185 R      0.971*        9.971 +- 1.661
   193 G      0.710         7.462 +- 4.372
   218 V      0.913         9.419 +- 2.723
   219 L      0.883         9.128 +- 3.114
   220 P      0.982*        10.074 +- 1.357
   221 R      0.996**       10.208 +- 0.786
   222 T      0.865         8.954 +- 3.308
   223 V      0.929         9.573 +- 2.484
   224 L      0.990*        10.149 +- 1.080
   226 R      0.977*        10.028 +- 1.513
   227 T      0.865         8.954 +- 3.308
   228 V      0.913         9.419 +- 2.723
   229 L      0.997**       10.213 +- 0.755
   231 R      0.986*        10.108 +- 1.239
   232 T      0.986*        10.115 +- 1.214
   234 L      0.988*        10.128 +- 1.165
   236 W      0.989*        10.139 +- 1.123
   237 T      0.991**       10.158 +- 1.039
   238 V      0.996**       10.206 +- 0.801
   239 L      0.988*        10.135 +- 1.138
   240 P      0.840         8.709 +- 3.548



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:   0.401  0.273  0.162  0.086  0.042  0.020  0.009  0.004  0.002  0.001
w2:   0.000  0.000  0.000  0.000  0.000  0.000  0.005  0.032  0.176  0.787

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.001 0.001 0.000 0.000
 0.000 0.000 0.001 0.002 0.001 0.000 0.000
 0.000 0.000 0.000 0.000 0.003 0.005 0.002 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.002 0.011 0.010 0.003 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008 0.032 0.019 0.004 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.029 0.079 0.027 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 0.009 0.082 0.152 0.032 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 0.004 0.033 0.177 0.224 0.031 0.003 0.000 0.000

sum of density on p0-p1 =   1.000000
