
seed used = 139991325

K12                                  ATG AAA CCA ACG TCG GTG ATC ATT ATG GAT ACT CAT CCT ATC ATC AGA ATG TCT ATT GAA GTT CTG TTG CAA AAA AAC AGT GAA TTG CAG ATT GTC CTG AAA ACG GAT GAT TAT CGC ATA ACC ATC GAT TAT CTC CGA ACC CGT CCT GTT GAT TTA ATC ATT ATG GAT ATA GAC TTG CCC GGA ACA GAC GGT TTT ACC TTC CTG AAA AGG ATC AAA CAA ATC CAG AGC ACA GTG AAA GTG TTA TTT TTA TCA TCG AAA TCA GAA TGC TTT TAT GCT GGC AGA GCG ATA CAA GCT GGT GCT AAC GGT TTT GTC AGT AAA TGC AAT GAT CAG AAT GAT ATT TTT CAT GCC GTT CAG ATG ATC CTC TCC GGA TAC 
Shig4337                             ATG AAA CCA ACG TCG GTG ATC ATT ATG GAT ACT CAT CCT ATC ATC AGA ATG TCT ATT GAA GTT CTG TTG CAA AAA AAC AGT GAA TTG CAG ATT GTC CTG AAA ACG GAT GAT TAC CGC ATA ACC ATC GAT TAT CTC CGA ACC CGT CCT GTT GAT TTA ATC ATT ATG GAT ATA GAC TTG CCC GGA ACA GAC GGT TTT ACC TTC CTG AAA AGG GTA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG CTG CCA ACT TAC 
O157                                 ATG AAA CCA ACG TCG GTG ATC ATT ATG GAT ACT CAT CCT ATC ATC AGA ATG TCT ATT GAA GTT CTG TTG CAA AAA AAC AGT GAA TTG CAG ATT GTC CTG AAA ACG GAT GAT TAC CGC ATA ACC ATC GAT TAT CTC CGA ACC CGT CCT GTT GAT TTA ATC ATT ATG GAT ATA GAC TTG CCC GGA ACA GAC GGT TTT ACC TTC CTG AAA AGG ATC AAA CAA ATC CAG AGC ACA GTG AAA GTG TTA TTT TTA TCA TCG AAA TCA GAA TGC TTT TAT GCT GGC AGA GCG ATA CAA GCT GGT GCT AAC GGT TTT GTC AGT AAA TGC AAT GAT CAG AAT GAT ATT TTT CAT GCC GTT CAG ATG ATC CTC TCC GGA TAC 
EDL933                               ATG AAA CCA ACG TCG GTG ATC ATT ATG GAT ACT CAT CCT ATC ATC AGA ATG TCT ATT GAA GTT CTG TTG CAA AAA AAC AGT GAA TTG CAG ATT GTC CTG AAA ACG GAT GAT TAC CGC ATA ACC ATC GAT TAT CTC CGA ACC CGT CCT GTT GAT TTA ATC ATT ATG GAT ATA GAC TTG CCC GGA ACA GAC GGT TTT ACC TTC CTG AAA AGG ATC AAA CAA ATC CAG AGC ACA GTG AAA GTG TTA TTT TTA TCA TCG AAA TCA GAA TGC TTT TAT GCT GGC AGA GCG ATA CAA GCT GGT GCT AAC GGT TTT GTC AGT AAA TGC AAT GAT CAG AAT GAT ATT TTT CAT GCC GTT CAG ATG ATC CTC TCC GGA TAC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0535.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 124
# site patterns = 76
    4    4    1    2    1    1    5    4    6    1    1    2    1    1    2
    2    3    3    1    1    1    1    1    1    1    2    3    1    1    1
    1    1    2    1    1    1    1    1    1    1    1    4    2    1    3
    1    1    2    2    4    2    1    1    2    1    3    1    1    1    1
    2    1    1    1    2    2    1    1    1    1    1    1    1    1    1
    1

K12                                  ATG AAA CCA ACG TCG GTG ATC ATT GAT ACT CAT CCT AGA TCT GAA GTT CTG TTG CAA AAC AGT CAG GTC TAT CGC ATA ACC TAT CTC CGA CGT TTA GAC CCC GGA ACA GGT TTT TTC AGG ATC AAA CAA ATC CAG AGC ACA GTG TTA TTT TCA TCG GAA TGC TAT GCT GGC AGA GCG ATA GGT AAC GTC AGT AAT GAT ATT CAT GCC GTT ATG ATC CTC TCC GGA TAC 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.A --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ..G ..G C.A ACT ... 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 



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

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

#1: K12            
position  1:    T:0.19355    C:0.16935    A:0.37903    G:0.25806
position  2:    T:0.37097    C:0.18548    A:0.30645    G:0.13710
position  3:    T:0.33065    C:0.23387    A:0.24194    G:0.19355

#2: Shig4337       
position  1:    T:0.14474    C:0.21053    A:0.42105    G:0.22368
position  2:    T:0.42105    C:0.19737    A:0.27632    G:0.10526
position  3:    T:0.30263    C:0.23684    A:0.22368    G:0.23684

#3: O157           
position  1:    T:0.19355    C:0.16935    A:0.37903    G:0.25806
position  2:    T:0.37097    C:0.18548    A:0.30645    G:0.13710
position  3:    T:0.32258    C:0.24194    A:0.24194    G:0.19355

#4: EDL933         
position  1:    T:0.19355    C:0.16935    A:0.37903    G:0.25806
position  2:    T:0.37097    C:0.18548    A:0.30645    G:0.13710
position  3:    T:0.32258    C:0.24194    A:0.24194    G:0.19355

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      16 | Ser S TCT       4 | Tyr Y TAT       8 | Cys C TGT       0
      TTC       4 |       TCC       3 |       TAC       7 |       TGC       6
Leu L TTA      10 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG      12 |       TCG       7 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       8 | His H CAT       7 | Arg R CGT       4
      CTC       7 |       CCC       4 |       CAC       0 |       CGC       4
      CTA       0 |       CCA       5 | Gln Q CAA      10 |       CGA       4
      CTG      13 |       CCG       0 |       CAG      13 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      19 | Thr T ACT       5 | Asn N AAT       6 | Ser S AGT       7
      ATC      29 |       ACC      12 |       AAC       7 |       AGC       3
      ATA      11 |       ACA       7 | Lys K AAA      28 | Arg R AGA       7
Met M ATG      20 |       ACG       8 |       AAG       0 |       AGG       4
------------------------------------------------------------------------------
Val V GTT      11 | Ala A GCT       9 | Asp D GAT      30 | Gly G GGT      10
      GTC       7 |       GCC       3 |       GAC       8 |       GGC       3
      GTA       1 |       GCA       0 | Glu E GAA      11 |       GGA       7
      GTG      10 |       GCG       3 |       GAG       0 |       GGG       0
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.18527    C:0.17634    A:0.38616    G:0.25223
position  2:    T:0.37946    C:0.18750    A:0.30134    G:0.13170
position  3:    T:0.32143    C:0.23884    A:0.23884    G:0.20089

Codon frequencies under model, for use in evolver:
  0.02330519  0.01731705  0.01731705  0.01456574
  0.01151550  0.00855666  0.00855666  0.00719719
  0.01850706  0.01375177  0.00000000  0.00000000
  0.00808827  0.00601003  0.00000000  0.00505517
  0.02218204  0.01648249  0.01648249  0.01386378
  0.01096054  0.00814429  0.00814429  0.00685034
  0.01761515  0.01308904  0.01308904  0.01100947
  0.00769847  0.00572039  0.00572039  0.00481155
  0.04857587  0.03609457  0.03609457  0.03035992
  0.02400219  0.01783496  0.01783496  0.01500137
  0.03857496  0.02866333  0.02866333  0.02410935
  0.01685868  0.01252694  0.01252694  0.01053668
  0.03172875  0.02357622  0.02357622  0.01983047
  0.01567773  0.01164943  0.01164943  0.00979858
  0.02519636  0.01872229  0.01872229  0.01574772
  0.01101174  0.00818234  0.00818234  0.00688234



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             0.3083 (0.0301 0.0976)
O157                 0.0000 (0.0000 0.0122) 0.3941 (0.0301 0.0763)
EDL933               0.0000 (0.0000 0.0122) 0.3941 (0.0301 0.0763)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, 4));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):   -542.499575     +0.000000
   5..6     6..1     6..2     5..7     7..3     7..4  
  0.00000  0.00994  0.69770  0.00000  0.00000  0.00000  0.68564  0.96190  0.00000  0.10624 167.95378
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.70765

((1: 0.009938, 2: 0.697705): 0.000000, (3: 0.000004, 4: 0.000004): 0.000000);

((K12: 0.009938, Shig4337: 0.697705): 0.000000, (O157: 0.000004, EDL933: 0.000004): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  0.68564


dN/dS for site classes (K=3)

p:   0.96190  0.00000  0.03810
w:   0.10624  1.00000167.95378

dN & dS for each branch

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

   5..6       0.000     82.1    289.9   6.5007   0.0000   0.0000    0.0    0.0
   6..1       0.010     82.1    289.9   6.5007   0.0041   0.0006    0.1    1.2
   6..2       0.698     82.1    289.9   6.5007   0.2860   0.0440    3.6   82.9
   5..7       0.000     82.1    289.9   6.5007   0.0000   0.0000    0.0    0.0
   7..3       0.000     82.1    289.9   6.5007   0.0000   0.0000    0.0    0.0
   7..4       0.000     82.1    289.9   6.5007   0.0000   0.0000    0.0    0.0


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

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

    71 I      0.946         158.865
   122 S      0.984*        165.253
   123 G      1.000**       167.949


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

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

   123 G      0.872         6.398 +- 3.296



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:   0.216  0.183  0.150  0.119  0.094  0.073  0.057  0.045  0.035  0.028
w2:   0.076  0.066  0.068  0.074  0.083  0.095  0.109  0.124  0.142  0.162

Posterior for p0-p1 (see the ternary graph)

 0.011
 0.004 0.010 0.014
 0.001 0.003 0.005 0.013 0.018
 0.001 0.001 0.002 0.004 0.007 0.017 0.023
 0.000 0.001 0.001 0.001 0.002 0.005 0.009 0.023 0.029
 0.000 0.000 0.001 0.001 0.001 0.002 0.003 0.007 0.013 0.030 0.037
 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.003 0.004 0.010 0.018 0.039 0.044
 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.002 0.004 0.006 0.013 0.025 0.050 0.051
 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.005 0.008 0.018 0.034 0.062 0.055
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.004 0.007 0.011 0.025 0.045 0.073 0.057

sum of density on p0-p1 =   1.000000
