
seed used = 140001921

K12                                  ATG CGT TTA GTG AAG CCA GTA ATG AAG AAA CCG CTC CGC CAG CAA AAC CGC CAG ATT ATT AGC TAT GTC CCA CGC ACG GAA CCC GCG CCG CCA GAA CAT GCG ATA AAG ATG GAT TCG TTT CGT GAT GTC TGG ATG CTG CGT GGC AAA TAT GTT GCG TTT GTA CTG ATG GGA GAG TCA TTT CTG CGC TCA CCG GCG TTT ACT GTG CCT GAA TCT GCC CAA CGT TGG GCA AAT CAG ATC CGC CAG GAA GGG GAA GTG ACT GAG 
S2457T                               ATG CGT TTA GTG AAG CCA GTA ATG AAG AAA CCG CTC CGC CAG CAA AAC CGC CAG ATT ATT AGC TAT GTC CCA CGC ACG GAA CCC GCG CCG CCA GAA CAT GCG ATA AAG ATG GAT TCG TTT CGT GAT GTC TGG ATG CTG CGT GGC AAA TAT GTT GCG TTT GTA CTG ATG GGA GAG TCA TTT CTG CGC TCA CCG GCG TTT ACT GTG CCT GAA TCT GCC CAA CGT TGG GCA AAT CAG ATC CGC CAG GAA GGG GAA GTG ACT GAG 
CFT073                               ATG CGT TTA GTG AAG CCA GTA ATG AAG AAA CCG CTC CGT CAG CAA AAC CGC CAG ATT ATT AGC TAT GTC CCA CGC ACG GAA CCC GCG CCG CCA GAA CAT GCG ATA AAG ATG GAT TCG TTT CGT GAT GTC TGG ATG CTG CGT GGC AAA TAT GTT GCG TTT GTA CTG ATG GGG GAG TCA TTT CTG CGC TCA CCG GCG TTT ACT GTG CCT GAA TCC GCC CAG CGT TGG GCA AAT CAG ATT CGT CAG GAA AAT GAG GTC GAA GAA 
O157                                 ATG CGT TTA GTG AAG CCA GTA ATG AAG AAA CCG CTC CGC CAG CAA AAC CGC CAG ATT ATT AGC TAT GTC CCA CGC ACG GAA CCC GCG CCG CCA GAA CAT GCG ATA AAG ATG GAT TCG TTT CGT GAT GTC TGG ATG CTG CGT GGC AAA TAT GTT GCG TTT GTA CTG ATG GGA GAG TCA TTT CTG CGC TCA CCG GCG TTT ACT GTG CCT GAA TCC GCC CAG CGT TGG GCA AAT CAG ATC CGC CAG GAA GGG GAA GTG ACT GAG 
EDL933                               ATG CGT TTA GTG AAG CCA GTA ATG AAG AAA CCG CTC CGC CAG CAA AAC CGC CAG ATT ATT AGC TAT GTC CCA CGC ACG GAA CCC GCG CCG CCA GAA CAT GCG ATA AAG ATG GAT TCG TTT CGT GAT GTC TGG ATG CTG CGT GGC AAA TAT GTT GCG TTT GTA CTG ATG GGA GAG TCA TTT CTG CGC TCA CCG GCG TTT ACT GTG CCT GAA TCC GCC CAG CGT TGG GCA AAT CAG ATC CGC CAG GAA GGG GAA GTG ACT GAG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1731.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 87
# site patterns = 48
    5    4    1    2    3    3    2    2    3    1    2    4    1    1    3
    2    1    2    2    1    4    1    4    1    1    2    1    4    2    3
    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
    1    1    1

1       
K12                   ATG CGT TTA GTG AAG CCA GTA AAA CCG CTC CGC CAG CAA AAC CGC ATT AGC TAT GTC ACG GAA CCC GCG CAT ATA GAT TCG TTT TGG CTG GGC GTT GGA GAG TCA ACT CCT TCT GCC CAA GCA AAT ATC GGG GAA GTG ACT GAG 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ..C ... ..G ... ... ..T AAT ..G ..C GAA ..A 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ..G ... ... ... ... ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ..G ... ... ... ... ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.14943    C:0.32184    A:0.22989    G:0.29885
position  2:    T:0.29885    C:0.24138    A:0.28736    G:0.17241
position  3:    T:0.24138    C:0.16092    A:0.22989    G:0.36782

#2: S2457T         
position  1:    T:0.14943    C:0.32184    A:0.22989    G:0.29885
position  2:    T:0.29885    C:0.24138    A:0.28736    G:0.17241
position  3:    T:0.24138    C:0.16092    A:0.22989    G:0.36782

#3: CFT073         
position  1:    T:0.14943    C:0.32184    A:0.22989    G:0.29885
position  2:    T:0.29885    C:0.22989    A:0.31034    G:0.16092
position  3:    T:0.26437    C:0.14943    A:0.21839    G:0.36782

#4: O157           
position  1:    T:0.14943    C:0.32184    A:0.22989    G:0.29885
position  2:    T:0.29885    C:0.24138    A:0.28736    G:0.17241
position  3:    T:0.22989    C:0.17241    A:0.21839    G:0.37931

#5: EDL933         
position  1:    T:0.14943    C:0.32184    A:0.22989    G:0.29885
position  2:    T:0.29885    C:0.24138    A:0.28736    G:0.17241
position  3:    T:0.22989    C:0.17241    A:0.21839    G:0.37931

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      20 | Ser S TCT       2 | Tyr Y TAT      10 | Cys C TGT       0
      TTC       0 |       TCC       3 |       TAC       0 |       TGC       0
Leu L TTA       5 |       TCA      10 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       5 |       TAG       0 | Trp W TGG      10
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       5 | His H CAT       5 | Arg R CGT      22
      CTC       5 |       CCC       5 |       CAC       0 |       CGC      23
      CTA       0 |       CCA      15 | Gln Q CAA       7 |       CGA       0
      CTG      15 |       CCG      15 |       CAG      23 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      11 | Thr T ACT       9 | Asn N AAT       6 | Ser S AGT       0
      ATC       4 |       ACC       0 |       AAC       5 |       AGC       5
      ATA       5 |       ACA       0 | Lys K AAA      10 | Arg R AGA       0
Met M ATG      25 |       ACG       5 |       AAG      15 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       5 | Ala A GCT       0 | Asp D GAT      10 | Gly G GGT       0
      GTC      11 |       GCC       5 |       GAC       0 |       GGC       5
      GTA      10 |       GCA       5 | Glu E GAA      26 |       GGA       4
      GTG      14 |       GCG      20 |       GAG      10 |       GGG       5
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14943    C:0.32184    A:0.22989    G:0.29885
position  2:    T:0.29885    C:0.23908    A:0.29195    G:0.17011
position  3:    T:0.24138    C:0.16322    A:0.22299    G:0.37241

Codon frequencies under model, for use in evolver:
  0.01113122  0.00752682  0.01028312  0.01717388
  0.00890497  0.00602146  0.00822650  0.01373910
  0.01087434  0.00735313  0.00000000  0.00000000
  0.00633623  0.00428450  0.00000000  0.00977590
  0.02397493  0.01621162  0.02214827  0.03698989
  0.01917994  0.01296930  0.01771862  0.02959191
  0.02342166  0.01583751  0.02163716  0.03613628
  0.01364727  0.00922815  0.01260748  0.02105579
  0.01712495  0.01157973  0.01582019  0.02642135
  0.01369996  0.00926378  0.01265615  0.02113708
  0.01672976  0.01131250  0.01545511  0.02581163
  0.00974805  0.00659154  0.00900534  0.01503985
  0.02226244  0.01505365  0.02056625  0.03434776
  0.01780995  0.01204292  0.01645300  0.02747821
  0.02174869  0.01470626  0.02009164  0.03355512
  0.01267246  0.00856900  0.01170694  0.01955180



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               0.1460 (0.0263 0.1804) 0.1460 (0.0263 0.1804)
O157                 0.0000 (0.0000 0.0330) 0.0000 (0.0000 0.0330) 0.1881 (0.0263 0.1400)
EDL933               0.0000 (0.0000 0.0330) 0.0000 (0.0000 0.0330) 0.1881 (0.0263 0.1400)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, (4, 5)));   MP score: 11
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):   -407.082692     +0.000000
   6..7     7..1     7..2     6..8     8..3     8..9     9..4     9..5  
  0.00000  0.00000  0.00000  0.02472  0.23180  0.00000  0.00000  0.00000  5.51847  0.97513  0.00000  0.00000 18.45870
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.25654

((1: 0.000004, 2: 0.000004): 0.000000, (3: 0.231800, (4: 0.000004, 5: 0.000004): 0.000000): 0.024720);

((K12: 0.000004, S2457T: 0.000004): 0.000000, (CFT073: 0.231800, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.024720);

Detailed output identifying parameters

kappa (ts/tv) =  5.51847


dN/dS for site classes (K=3)

p:   0.97513  0.00000  0.02487
w:   0.00000  1.00000 18.45870

dN & dS for each branch

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

   6..7       0.000     82.2    178.8   0.4591   0.0000   0.0000    0.0    0.0
   7..1       0.000     82.2    178.8   0.4591   0.0000   0.0000    0.0    0.0
   7..2       0.000     82.2    178.8   0.4591   0.0000   0.0000    0.0    0.0
   6..8       0.025     82.2    178.8   0.4591   0.0060   0.0131    1.1    1.1
   8..3       0.232     82.2    178.8   0.4591   0.0564   0.1227   10.1   10.1
   8..9       0.000     82.2    178.8   0.4591   0.0000   0.0000    0.0    0.0
   9..4       0.000     82.2    178.8   0.4591   0.0000   0.0000    0.0    0.0
   9..5       0.000     82.2    178.8   0.4591   0.0000   0.0000    0.0    0.0


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

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

    83 G      1.000**       18.459
    86 T      1.000**       18.459


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

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

    83 G      0.969*        7.928 +- 2.373
    86 T      0.978*        7.997 +- 2.284



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:   0.897  0.092  0.010  0.001  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.005  0.012  0.027  0.049  0.076  0.107  0.138  0.168  0.196  0.221

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 0.002
 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 0.002 0.015
 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 0.002 0.019 0.104
 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 0.141 0.700

sum of density on p0-p1 =   1.000000
