
seed used = 139991789

K12                                  TTG CTG ATT TTG CGT AAA GAG GAT GCG AGT GCA TCC TCT GGG CAA AGC GAG TTA TCG CTT GTG CAG ATG GGA TTA AAG CAG GTA GTC GCC AGC AGC TTC TGG CTG GTA TTC GAG TTC CAG CAC TTC AAG GTG GGT TGC AAC GCC GCC CGG AAG TTC CCA GTG AAT GGA ATC GCC AAC GCG CAG CCC CAG CAG TGC GGC ACC TAC CGG AGC CAT AAC GGA AAG CTG AGT ATT GCT ATC GGT CAT TTT TGC CGG ATA CAC CAG CGT GCG CAC ACG CAC TTC GCC ATC GCT AAG ATT GCG GAA TTT AAC CCG GCT GTT CAT TGT CAC CAC GTC GTG TGG CAT CTC TTC TGG CGA ACA CAT TTG GGC GCG ATC CAA CTC TGC GTT 
S2457T                               TTG CTG ATT TTG CGT AAA GAG GAT GCG AGT GCA TCC TCT GGG CAA AGC GAG TTA TCG CTT GTG CAG ATG GGA TTA AAG CAG GTA GTC GCC AGC AGC TTC TGG CTG GTA TTC GAG TTC CAG CAC TTC AAG GTG GGT TGC AAC GCC GCC CGG AAG TTC CCA GTG AAT GGA ATC GCC AAC GCG CAG CCC CAG CAG TGC GGC ACC TAC CGG AGC CAT AAC GGA AAG CTG AGT ATT GCT ATC GGT CAT TTT TGC CGG ATA CAC CAG CGT GCG CAC ACG CAC TTC GCC ATC GCT AAG ATT GCG GAA TTT AAC CCG GCT GTT CAT TGT CAC CAC GTC GTG TGG CAT CTC TTC TGG CGA ACA CAT TTG GGC GCG ATC CAA CTC TGC GTT 
CFT073                               TTG ATA TTT GAG CGG AAA GAG GAT GCG AGT GCA TCC TCT GGG CAA AGC GAG TTA TCG CTT GTG CAG ATG GGA TTA AAG CAG GTA ATC GCC AGC AGC TTC TGG CTG GTA TTC GAG TTC CAG CAC TTC AAG GTG GGT TGC AAC GCC GCC CGG CAG TTC CCA GTG AAT GGA ATC GCC AAC GCG CAG CCC CAG CAG TGC GGC ACC TAC CGG AGC CAT AAC GGA AAG CTG AGT ATT GCT GTC GGT CAT TTT TGC CGG ATA CAC CAG CGT GCG CAC ACG CAC TTC GCC ATC GCT AAG ATT GCG GAA TTT AAC CCG GCT GTT CAT TGT CAC CAC GTC GTG TGG CAT CTC TTC TGG CGA ACA CAT TTG GGC GCG ATC CAA CTC TGC GTT 
O157                                 TTG CTG ATT TTG CAT AAA GAG GAT GCG AGT GCA TCC TCT GGG CAA AGC GAG TTA TCG CTT GTA CAG ATG GGA TTA AAG CAG GTA GTC GCC AGC AGC TTC TGG CTG GTA TTC GAG TTC CAG CAC TTC AAG GTG GGT TGC AAC GCC GCC CGG AAG TTC CCA GTG AAT GGA ATC GCC AAC GCG CAG TCC CAG CAG TGC GGC ACC TAC CGG AGC CAT AAC GGA AAG CTG AGT ATT GCT ATC GGT CAT TTT TGC CGG ATA CAC CAG CGT GCG CAC ACG CAC TTC GCC ATC GCT AAG ATT GCG GAA TTT AAC CCG GCT GTT CAT TGT CAC CAC GTC GTG TGG CAT CTC TTC TGG CGA ACA CAT TTG GGC GCG ATC CAA CTC TGC GTT 
EDL933                               TTG CTG ATT TTG CAT AAA GAG GAT GCG AGT GCA TCC TCT GGG CAA AGC GAG TTA TCG CTT GTA CAG ATG GGA TTA AAG CAG GTA GTC GCC AGC AGC TTC TGG CTG GTA TTC GAG TTC CAG CAC TTC AAG GTG GGT TGC AAC GCC GCC CGG AAG TTC CCA GTG AAT GGA ATC GCC AAC GCG CAG TCC CAG CAG TGC GGC ACC TAC CGG AGC CAT AAC GGA AAG CTG AGT ATT GCT ATC GGT CAT TTT TGC CGG ATA CAC CAG CGT GCG CAC ACG CAC TTC GCC ATC GCT AAG ATT GCG GAA TTT AAC CCG GCT GTT CAT TGT CAC CAC GTC GTG TGG CAT CTC TTC TGG CGA ACA CAT TTG GGC GCG ATC CAA CTC TGC GTT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0609.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 127
# site patterns = 60
    2    1    1    1    1    1    3    1    5    2    1    1    1    1    2
    4    2    1    1    1    7    1    3    4    2    1    5    7    3    2
    6    3    2    4    4    3    1    1    1    3    1    2    1    1    5
    2    3    1    2    1    1    1    1    1    2    1    1    2    1    1


1       
K12                   TTG CTG ATT TTG CGT AAA GAG GAT GCG AGT GCA TCC TCT GGG CAA AGC TTA TCG CTT GTG CAG ATG GGA AAG GTA GTC GCC TTC TGG CTG CAC GTG GGT TGC AAC CGG AAG CCA AAT ATC CCC GGC ACC TAC CAT ATT GCT ATC TTT ATA CGT ACG GAA CCG GTT TGT GTC CTC CGA ACA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... A.A T.. GA. ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... 
O157                  ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
EDL933                ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.20472    C:0.27559    A:0.22835    G:0.29134
position  2:    T:0.30709    C:0.18110    A:0.29134    G:0.22047
position  3:    T:0.20472    C:0.34646    A:0.12598    G:0.32283

#2: S2457T         
position  1:    T:0.20472    C:0.27559    A:0.22835    G:0.29134
position  2:    T:0.30709    C:0.18110    A:0.29134    G:0.22047
position  3:    T:0.20472    C:0.34646    A:0.12598    G:0.32283

#3: CFT073         
position  1:    T:0.20472    C:0.27559    A:0.22047    G:0.29921
position  2:    T:0.29921    C:0.18110    A:0.29921    G:0.22047
position  3:    T:0.19685    C:0.34646    A:0.13386    G:0.32283

#4: O157           
position  1:    T:0.21260    C:0.26772    A:0.22835    G:0.29134
position  2:    T:0.30709    C:0.18110    A:0.29921    G:0.21260
position  3:    T:0.20472    C:0.34646    A:0.13386    G:0.31496

#5: EDL933         
position  1:    T:0.21260    C:0.26772    A:0.22835    G:0.29134
position  2:    T:0.30709    C:0.18110    A:0.29921    G:0.21260
position  3:    T:0.20472    C:0.34646    A:0.13386    G:0.31496

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      11 | Ser S TCT       5 | Tyr Y TAT       0 | Cys C TGT       5
      TTC      35 |       TCC       7 |       TAC       5 |       TGC      20
Leu L TTA      10 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG      14 |       TCG       5 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT       5 | Pro P CCT       0 | His H CAT      27 | Arg R CGT       7
      CTC      10 |       CCC       3 |       CAC      30 |       CGC       0
      CTA       0 |       CCA       5 | Gln Q CAA      10 |       CGA       5
      CTG      14 |       CCG       5 |       CAG      36 |       CGG      16
------------------------------------------------------------------------------
Ile I ATT      14 | Thr T ACT       0 | Asn N AAT       5 | Ser S AGT      10
      ATC      20 |       ACC       5 |       AAC      20 |       AGC      20
      ATA       6 |       ACA       5 | Lys K AAA       5 | Arg R AGA       0
Met M ATG       5 |       ACG       5 |       AAG      24 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      10 | Ala A GCT      15 | Asp D GAT       5 | Gly G GGT      10
      GTC      10 |       GCC      25 |       GAC       0 |       GGC      10
      GTA      12 |       GCA       5 | Glu E GAA       5 |       GGA      15
      GTG      18 |       GCG      25 |       GAG      16 |       GGG       5
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.20787    C:0.27244    A:0.22677    G:0.29291
position  2:    T:0.30551    C:0.18110    A:0.29606    G:0.21732
position  3:    T:0.20315    C:0.34646    A:0.13071    G:0.31969

Codon frequencies under model, for use in evolver:
  0.01335051  0.02276832  0.00858987  0.02100895
  0.00791396  0.01349668  0.00509193  0.01245376
  0.01293761  0.02206414  0.00000000  0.00000000
  0.00949676  0.01619602  0.00000000  0.01494451
  0.01749726  0.02984030  0.01125793  0.02753445
  0.01037209  0.01768883  0.00667351  0.01632197
  0.01695611  0.02891740  0.01090975  0.02668287
  0.01244651  0.02122660  0.00800822  0.01958636
  0.01456420  0.02483816  0.00937076  0.02291885
  0.00863342  0.01472365  0.00555483  0.01358592
  0.01411376  0.02406997  0.00908094  0.02221002
  0.01036010  0.01766839  0.00666580  0.01630310
  0.01881209  0.03208263  0.01210390  0.02960352
  0.01115150  0.01901805  0.00717499  0.01754848
  0.01823027  0.03109038  0.01172955  0.02868794
  0.01338179  0.02282166  0.00860999  0.02105817



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                 
S2457T              -1.0000 (0.0000 0.0000)
CFT073               1.4612 (0.0258 0.0177) 1.4612 (0.0258 0.0177)
O157                 0.5809 (0.0068 0.0117) 0.5809 (0.0068 0.0117) 1.4562 (0.0346 0.0238)
EDL933               0.5809 (0.0068 0.0117) 0.5809 (0.0068 0.0117) 1.4562 (0.0346 0.0238)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, (4, 5)));   MP score: 10
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):   -579.110873     +0.000000
   6..7     7..1     7..2     6..8     8..3     8..9     9..4     9..5  
  0.00000  0.00000  0.00000  0.00000  0.23349  0.03730  0.00000  0.00000  8.27310  0.96589  0.00001  1.00000 229.89471
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.27081

((1: 0.000004, 2: 0.000004): 0.000000, (3: 0.233493, (4: 0.000004, 5: 0.000004): 0.037301): 0.000000);

((K12: 0.000004, S2457T: 0.000004): 0.000000, (CFT073: 0.233493, (O157: 0.000004, EDL933: 0.000004): 0.037301): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  8.27310


dN/dS for site classes (K=3)

p:   0.96589  0.00001  0.03409
w:   1.00000  1.00000229.89471

dN & dS for each branch

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

   6..7       0.000    110.6    270.4   8.8039   0.0000   0.0000    0.0    0.0
   7..1       0.000    110.6    270.4   8.8039   0.0000   0.0000    0.0    0.0
   7..2       0.000    110.6    270.4   8.8039   0.0000   0.0000    0.0    0.0
   6..8       0.000    110.6    270.4   8.8039   0.0000   0.0000    0.0    0.0
   8..3       0.233    110.6    270.4   8.8039   0.1048   0.0119    1.3   28.3
   8..9       0.037    110.6    270.4   8.8039   0.0167   0.0019    0.2    4.5
   9..4       0.000    110.6    270.4   8.8039   0.0000   0.0000    0.0    0.0
   9..5       0.000    110.6    270.4   8.8039   0.0000   0.0000    0.0    0.0


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

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

     2 L      0.978*        224.816
     4 L      0.997**       229.158
     5 R      0.978*        224.904


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

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

     2 L      0.937         7.272 +- 2.719
     3 I      0.766         6.057 +- 3.475
     4 L      0.957*        7.406 +- 2.579
     5 R      0.756         5.978 +- 3.502
    29 V      0.740         5.853 +- 3.537
    51 K      0.756         5.975 +- 3.501
    62 P      0.744         5.884 +- 3.528
    79 I      0.739         5.850 +- 3.537



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:   0.107  0.106  0.104  0.102  0.101  0.099  0.098  0.096  0.095  0.093
w2:   0.004  0.022  0.050  0.076  0.098  0.117  0.135  0.151  0.166  0.181

Posterior for p0-p1 (see the ternary graph)

 0.001
 0.012 0.004 0.001
 0.018 0.016 0.012 0.004 0.001
 0.015 0.018 0.019 0.016 0.012 0.003 0.001
 0.009 0.013 0.015 0.019 0.020 0.016 0.012 0.003 0.001
 0.006 0.008 0.010 0.014 0.016 0.020 0.020 0.016 0.011 0.003 0.001
 0.004 0.005 0.006 0.009 0.011 0.015 0.017 0.020 0.021 0.016 0.011 0.003 0.001
 0.003 0.004 0.004 0.006 0.007 0.009 0.011 0.015 0.018 0.021 0.021 0.015 0.010 0.002 0.000
 0.002 0.003 0.003 0.004 0.005 0.006 0.007 0.010 0.012 0.016 0.019 0.022 0.021 0.015 0.010 0.002 0.000
 0.002 0.002 0.002 0.003 0.003 0.004 0.005 0.007 0.008 0.011 0.013 0.017 0.020 0.022 0.022 0.015 0.009 0.002 0.000

sum of density on p0-p1 =   1.000000
