
seed used = 141415677

K12                                  ATA AAA ATA TAC ATT GCG CCT CCT GAA AAA ATA AAT TTT TTA TGC TAT TAC GTA TAT TTG TAT CTA TTT CAA TGG AAT GAC AAC GTG AAT ATT AAT TAC CCT GCT GAA TAT GAA ATT GGA GAT ATC GTC TTT ACA TGT ATA GGT GCT GCC TTA TTT GGT CAA ATA TCA GCT GCA TCA AAT TGC TGG AGT AAT CAC GTC GGG ATC ATT ATC GGT CAT AAC GGT GAA GAC TTC CTG GTT GCA GAA AGC CGG GTT CCC CTT TCA ACC ATC ACC ACG CTA TCT CGT TTT ATT AAA CGT TCG TCT AAT CAA CGC TAT GCT ATA AAG CGA TTA GAC GCT GGG CTG ACA GAA CGA CAA AAA CAA CGA ATT GTT GAA CAG GTT CCC TCC CGG CTA CGC AAA CTT TAC CAC ACC GGT TTT AAA TAC GAA TCT TCG CGC CAG TTC TGT TCA AAA TTT GTT TTT GAT ATT TAT AAA GAA GCG CTA TGT ATT CCG GTG GGT GAA ATA GAG ACG TTT GGA GAA TTG TTA AAT AGC AAT CCG AAT GCA AAA CTC ACT TTC TGG AAA TTC TGG TTC CTG GGT TCT ATT CCG TGG GAG CGT AAA ACC GTC ACG CCA GCC AGT TTG TGG CAT CAT CCG GGT TTG GTG TTG ATT CAT GCG GAG GGA GTG GAA ACG CCT CAG CCG GAA CTG ACC GAG GCG GTA 
Shig4337                             TTG CGA CTC CTG AAA AAT --- --- --- --- --- AAT TTT TTA TGC TAT TAC GTA TAT TTG TAT CTA TTT CAA TGG AAT GAC AAC GTG AAT ATT AAT TAC CCT GCT GAA TAT GAA ATT GGA GAT ATC GTC TTT ACA TGT ATA GGT GCT GCC TTA TTT GGT CAA ATA TCA GCT GCA TCA AAT TGC TGG AGT AAT CAC GTC GGG ATC ATT ATC GGT CAT AAC GGT GAA GAC TTC CTG GTT GCA GAA AGC CGG GTT CCC CTT TCA ACC ATC ACC ACG CTA TCT CGT TTT ATT AAA CGT TCG TCT AAT CAA CGC TAT GCT ATA AAG CGA TTA GAC GCT GGG CTG ACA GAA CAA CAA AAA CAA CGA ATT GTT GAA CAG GTT CCC TCC CGG CTA CGC AAA CTT TAC CAC ACG GGT TTT AAA TAC GAA TCT TCG CGC CAG TTC TGT TCA AAA TTT GTC TTT GAT ATT TAT AAA GAG GCG CTA TGT ATT CCG GTG GGT GAA ATA GAG ACG TTT GGA CAA CTG TTA AAT AGC AAT CCG AAT GCA AAA CTC ACT TTC TGG AAA TTC TGG TTC TTA GGT TCT ATT CCG TGG GAG CGT AAA ACC GTC ACG CCA GCC AGT TTG TGG CAT CAT CCG GGT TTG GTG TTG ATT CAC GCG GAG GGA GTT GAA ACG CCT CAG CCG GAA CTG ACC GAG GCG GTA 
CFT073                               TTG CGA CCC CTG AAA AAA --- --- --- --- ATA AAT TTT TTA TGC TAT TAC GTA TAT TCA TAT CTA TTT CAA TGG AAT GAC AAC GTG AAT ATT AAT TAT CCT GCT GAA TAT GAA ATT GGT GAT ATC GTC TTT ACA TGT ATA AGT GCT GCC TTA TTT GGT CAA ATA TCA GCT GCA TCA AAT TGC TGG AGT AAT CAC GTC GGG ATC ATT ATC GGT CAT AAC GGT GAA GAC TTT CTG GTT GCA GAA AGC CGT GTT CCC CTC TCA ACC ATC ACT ACG CTA TCC CGT TTT ATT AAA CGC TCT GCT AAT CAA CGC TAT GCT ATA AAG CGA TTA GAC GCC GGA CTA ACA GAA CAA CAA AAT CAA CGA ATT GTT GAA CAG GTT CCT TCC CGG CTA CGC AAA ATT TAC CAC ACC GGT TTT AAA TAC GAA TCT TCG CGC CAG TTC TGT TCA AAA TTT GTT TTT GAT ATT TAT AAA GAG GCG CTA TGT ATT CCG GTG GGT GAA ATA GAG ACG TTT GGA GAA TTG TTA AAT AGC AAT CCA AAT GCA AAA CTC ACT TTC TGG AAA TTC TGG TTC TTA GGT TCT ATT CCG TGG GAG CGT AAA ACC GTC ACG CCA GCC AGT TTG TGG CAT CAT CCG GGT TTG GTG TTG ATT CAC GCG GTG GGA GTT GAA ACG CCT CAG CCT GAA CTG ACC GAG GCG GTA 
O157                                 ATA AAA ATA TAC ATT GCG CCT CCT GAA AAA ATA AAT TTT TTA TGC TAT TAC GTA TAT TCG TAT CTA TTT CAA TGG AAT GAC AAC GTG AAT ATT AAT TAC CCT GCT GAA TAT GAA ATT GGA GAT AAA GTC TTT ACA TGT ATA GGT GCT GCC TTA TTT GGT CAA ATA TCA GCT GCA TCA AAT TGC TGG AGT AAT CAC GTC GGG ATC ATT ATC GGT CAT AAC GGT GAA GAC TTC CTG GTT GCA GAA AGC CGG GTT CCC CTT TCA ACC ATC ACC ACG CTA TCT CGT TTT ATT AAA CGT TCG TCT AAT CAA CGC TAT GCT ATA AAG CGA TTA GAC GCT GGG CTG ACA GAA CAA CAA AAA CAA CGA ATT GTT GAA CAG GTT CCC TCC CGG CTA CGC AAA CTT TAC CAC ACC GGT TTT AAA TAC GAA TCT TCG CGC CAG TTC TGT TCA AAA TTT GTT TTT GAT ATT TAT AAA GAA GCG CTA TGT ATT CCG GTG GGT GAA ATA GAG ACG TTT GGA GAA TTG TTA AAT AGC AAT CCG AAT GCA AAA CTC ACT TTC TGG AAA TTC TGG TTC CTG GGT TCT ATT CCG TGG GAG CGT AAA ACC GTC ACG CCA GCC AGT TTG TGG CAT CAT CCA GGT TTG GTG TTG ATT CAT GCG GAG GGA GTG GAA ACG CCT CAG CCG GAA CTG ACC GAG GCG GTA 
EDL933                               ATA AAA ATA TAC ATT GCG CCT CCT GAA AAA ATA AAT TTT TTA TGC TAT TAC GTA TAT TCG TAT CTA TTT CAA TGG AAT GAC AAC GTG AAT ATT AAT TAC CCT GCT GAA TAT GAA ATT GGA GAT AAA GTC TTT ACA TGT ATA GGT GCT GCC TTA TTT GGT CAA ATA TCA GCT GCA TCA AAT TGC TGG AGT AAT CAC GTC GGG ATC ATT ATC GGT CAT AAC GGT GAA GAC TTC CTG GTT GCA GAA AGC CGG GTT CCC CTT TCA ACC ATC ACC ACG CTA TCT CGT TTT ATT AAA CGT TCG TCT AAT CAA CGC TAT GCT ATA AAG CGA TTA GAC GCT GGG CTG ACA GAA CAA CAA AAA CAA CGA ATT GTT GAA CAG GTT CCC TCC CGG CTA CGC AAA CTT TAC CAC ACC GGT TTT AAA TAC GAA TCT TCG CGC CAG TTC TGT TCA AAA TTT GTT TTT GAT ATT TAT AAA GAA GCG CTA TGT ATT CCG GTG GGT GAA ATA GAG ACG TTT GGA GAA TTG TTA AAT AGC AAT CCG AAT GCA AAA CTC ACT TTC TGG AAA TTC TGG TTC CTG GGT TCT ATT CCG TGG GAG CGT AAA ACC GTC ACG CCA GCC AGT TTG TGG CAT CAT CCA GGT TTG GTG TTG ATT CAT GCG GAG GGA GTG GAA ACG CCT CAG CCG GAA CTG ACC GAG GCG GTA 


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b1862.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 228
# site patterns = 98
    1    1    1    1    1    1    2    1    1    1   10    9    4    2    6
    3    2    1    4    5    6    3    2    3    9    1    2    4   10    1
    2    1    3    2    3    4    1    2    7    4    3    2    2    1    3
    3    1    2    4    2    1    1    1    3    1    4    1    2    8    1
    1    1    3    1    2    1    1    1    1    1    3    1    1    1    1
    1    2    1    4    1    1    3    2    3    2    1    1    1    1    1
    1    1    3    1    1    1    1    1

K12                                  ATA AAA ATA TAC ATT GCG CCT GAA AAA ATA AAT TTT TTA TGC TAT TAC GTA TTG CTA CAA TGG GAC AAC GTG ATT TAC CCT GCT GAA GGA GAT ATC GTC ACA TGT ATA GGT GCC GGT TCA GCA AGT CAC GGG ATC CAT TTC CTG GTT AGC CGG CCC CTT ACC ACC ACG TCT CGT AAA CGT TCG TCT CGC AAG CGA GCT GGG CTG CGA AAA CAG CCC TCC CGG CTT ACC TCT TCG TTC GTT GAA GCG CCG GAG GGA GAA TTG CCG CTC ACT CTG CCA TTG CCG CAT GAG GTG CCG 
Shig4337                             T.G CG. C.C CTG .AA AAT --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ..G ... ... ... ..C ..G ... ... ... ... C.. C.. ... ... ... T.A ... ... ... ..C ... ..T ... 
CFT073                               T.G CG. CCC CTG .AA AAA --- --- --- ... ... ... ... ... ... ... ... .CA ... ... ... ... ... ... ... ..T ... ... ... ..T ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ..T ... ... ... ..T ... ..C ... ..T ... ..C ... ... ..C ..T G.. ... ... ... ..C ..A ..A .A. ..T ... ..T ... ... A.. ... ... ... ... ... ..G ... ... ... ... ... ... ..A ... ... T.A ... ... ... ..C .T. ..T ..T 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... .AA ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... .AA ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... 



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

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

#1: K12            
position  1:    T:0.24561    C:0.21053    A:0.26754    G:0.27632
position  2:    T:0.30263    C:0.21491    A:0.31140    G:0.17105
position  3:    T:0.34211    C:0.18421    A:0.27193    G:0.20175

#2: Shig4337       
position  1:    T:0.25112    C:0.22422    A:0.25561    G:0.26906
position  2:    T:0.30493    C:0.20628    A:0.31390    G:0.17489
position  3:    T:0.33632    C:0.19283    A:0.26009    G:0.21076

#3: CFT073         
position  1:    T:0.25000    C:0.20982    A:0.26786    G:0.27232
position  2:    T:0.30357    C:0.21429    A:0.30804    G:0.17411
position  3:    T:0.35714    C:0.19196    A:0.27679    G:0.17411

#4: O157           
position  1:    T:0.24561    C:0.21053    A:0.26754    G:0.27632
position  2:    T:0.29386    C:0.21930    A:0.32018    G:0.16667
position  3:    T:0.34211    C:0.17982    A:0.28070    G:0.19737

#5: EDL933         
position  1:    T:0.24561    C:0.21053    A:0.26754    G:0.27632
position  2:    T:0.29386    C:0.21930    A:0.32018    G:0.16667
position  3:    T:0.34211    C:0.17982    A:0.28070    G:0.19737

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      46 | Ser S TCT      19 | Tyr Y TAT      31 | Cys C TGT      15
      TTC      24 |       TCC       6 |       TAC      22 |       TGC      10
Leu L TTA      22 |       TCA      21 | *** * TAA       0 | *** * TGA       0
      TTG      23 |       TCG      11 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT       8 | Pro P CCT      18 | His H CAT      18 | Arg R CGT      15
      CTC       7 |       CCC      10 |       CAC      12 |       CGC      16
      CTA      21 |       CCA       8 | Gln Q CAA      30 |       CGA      13
      CTG      20 |       CCG      21 |       CAG      15 |       CGG       9
------------------------------------------------------------------------------
Ile I ATT      49 | Thr T ACT       6 | Asn N AAT      52 | Ser S AGT      11
      ATC      18 |       ACC      23 |       AAC      10 |       AGC      10
      ATA      30 |       ACA      10 | Lys K AAA      55 | Arg R AGA       0
Met M ATG       0 |       ACG      21 |       AAG       5 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      26 | Ala A GCT      25 | Asp D GAT      10 | Gly G GGT      40
      GTC      16 |       GCC      11 |       GAC      15 |       GGC       0
      GTA      10 |       GCA      15 | Glu E GAA      60 |       GGA      15
      GTG      19 |       GCG      18 |       GAG      21 |       GGG       9
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.24757    C:0.21309    A:0.26525    G:0.27409
position  2:    T:0.29973    C:0.21485    A:0.31477    G:0.17065
position  3:    T:0.34394    C:0.18568    A:0.27409    G:0.19629

Codon frequencies under model, for use in evolver:
  0.02681572  0.01447635  0.02136986  0.01530357
  0.01922189  0.01037686  0.01531822  0.01096982
  0.02816046  0.01520231  0.00000000  0.00000000
  0.01526677  0.00824170  0.00000000  0.00871265
  0.02308068  0.01246000  0.01839334  0.01317200
  0.01654455  0.00893151  0.01318461  0.00944188
  0.02423811  0.01308484  0.01931572  0.01383255
  0.01314033  0.00709375  0.01047172  0.00749911
  0.02873113  0.01551038  0.02289627  0.01639669
  0.02059488  0.01111806  0.01641237  0.01175338
  0.03017193  0.01628819  0.02404446  0.01721894
  0.01635725  0.00883039  0.01303534  0.00933499
  0.02968884  0.01602739  0.02365948  0.01694324
  0.02128138  0.01148866  0.01695945  0.01214516
  0.03117766  0.01683113  0.02484595  0.01779290
  0.01690249  0.00912474  0.01346985  0.00964615



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                 
Shig4337             0.3129 (0.0244 0.0780)
CFT073               0.1982 (0.0354 0.1787) 0.1364 (0.0178 0.1307)
O157                 0.7198 (0.0067 0.0093) 0.3087 (0.0274 0.0888) 0.1795 (0.0344 0.1914)
EDL933               0.7198 (0.0067 0.0093) 0.3087 (0.0274 0.0888) 0.1795 (0.0344 0.1914)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, (4, 5)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1209.770365     +0.000000
   6..7     7..1     7..2     6..8     8..3     8..9     9..4     9..5  
  0.00250  0.00722  0.30561  0.00008  0.87031  0.01611  0.00000  0.00000  1.97962  0.96340  0.00000  0.08340 67.16604
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.20185

((1: 0.007221, 2: 0.305613): 0.002505, (3: 0.870310, (4: 0.000004, 5: 0.000004): 0.016110): 0.000079);

((K12: 0.007221, Shig4337: 0.305613): 0.002505, (CFT073: 0.870310, (O157: 0.000004, EDL933: 0.000004): 0.016110): 0.000079);

Detailed output identifying parameters

kappa (ts/tv) =  1.97962


dN/dS for site classes (K=3)

p:   0.96340  0.00000  0.03660
w:   0.08340  1.00000 67.16604

dN & dS for each branch

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

   6..7       0.003    169.3    514.7   2.5384   0.0010   0.0004    0.1    0.5
   7..1       0.007    169.3    514.7   2.5384   0.0028   0.0011    0.2    1.5
   7..2       0.306    169.3    514.7   2.5384   0.1199   0.0472    8.0   61.7
   6..8       0.000    169.3    514.7   2.5384   0.0000   0.0000    0.0    0.0
   8..3       0.870    169.3    514.7   2.5384   0.3413   0.1345   22.8  175.7
   8..9       0.016    169.3    514.7   2.5384   0.0063   0.0025    0.4    3.3
   9..4       0.000    169.3    514.7   2.5384   0.0000   0.0000    0.0    0.0
   9..5       0.000    169.3    514.7   2.5384   0.0000   0.0000    0.0    0.0


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

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

     1 I      1.000**       67.135
     2 K      1.000**       67.162
     3 I      1.000**       67.166
     4 Y      1.000**       67.166
     5 I      1.000**       67.157
     6 A      1.000**       67.166
    20 L      0.717         48.182
    42 I      0.740         49.743
   188 L      0.634         42.597


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

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

     1 I      0.991**       10.053 +- 1.081
     2 K      0.998**       10.113 +- 0.791
     3 I      0.997**       10.109 +- 0.810
     4 Y      1.000**       10.133 +- 0.660
     5 I      0.993**       10.073 +- 0.993
     6 A      1.000**       10.132 +- 0.666
    20 L      0.733         7.569 +- 4.298
    42 I      0.687         7.129 +- 4.491



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:   0.953  0.047  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.000  0.000  0.002  0.011  0.055  0.216  0.716

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.066
 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 0.161 0.769

sum of density on p0-p1 =   1.000000
