
seed used = 140024389

K12                                  GTG CAG GCC AAA ATT GCG GCA TCA AAT ACG GGT GAA CTG GAT GCC CTG CAA CAG CTG GGA TTC TCC CTG GTA GAA GGT GAA GTT GAT TTG GCG CTA CCC GTG AAC AAT GCC AGT GAT AGC GGT GCT GTA GTG GCA CAA GAG ACC GAT ATT CCC GCA TTA CGT CAG TTA GCC AGC GCC GCA TTT GCG CAA AGC CGT TTT CGT GCG CCG TGG TAT GCG CCT GAC GCC AGC AGT CGC TTT TAT GCA CAG TGG ATT GAA AAT GCC GTG CGC GGC ACC TTT GAT CAT CAA TGT CTG ATT TTA CGT GCG GCG TCC GGC GAT ATT CGC GGC TAT GTC TCT TTA CGG GAA CTC AAT GCG ACA GAT GCG CGA ATT GGC CTG CTG GCT GGA CGC GGT GCA GGT GCT GAG CTG ATG CAA ACG GCG CTA AAC TGG GCG TAT GCT CGC GGT AAA ACA ACT TTG CGG GTG GCG ACC CAA ATG GGC AAC ACC GCC GCG CTT AAA CGA TAC ATA CAA AGT GGT GCG AAT GTA GAA AGC ACC GCG TAC TGG TTA TAC AGG 
S2457T                               GTG CAG GCC AAA ATT GCG GCA TCA AAT ACG GGG GAA CTG GAT GCC CTG CAA CAG CTG GGA TTC TCC CTG GTA GAA GGT GAA GTT GAT TTG GCG CTA CCC GTG AAC AAT GTC AGT GAT AGC GGT GCT GTC GTG GCA CAA GAG ACC GAT ATT CCC GCA TTA CGT CAG TTA GCT AGC GCC GCA TTT GCG CAA AGC CGT TTT CGT GCG CCG TGG TAT GCG CCT GAC GCC AGC GGT CGC TTT TAT GCA CAG TGG ATT GAA AAT GCC GTG CGC GGC ACC TTT GAT CAT CAA TGT CTG ATT CTA CGT GCG GCG TCC GGC GAT ATT CGC GGC TAT GTC TCT TTA CGG GAA CTC AAT GCG ACA GAT GCG CGA ATT GGC CTG CTG GCT GGA CGC GGT GCA GGT GCT GAG CTG ATG CAA ACG GCG CTA AAC TGG GCG TAT GCT CGC GGT AAA ACA ACT TTG CGG GTG GCG ACC CAA ATG GGC AAC ACC GCC GCG CTT AAA CGA TAC ATA CAA AGT GGT GCG AAT GTA GAA AGC ACC GCG TAC TGG TTA TAC AGG 
Shig4337                             GTG CAG GCC AAA ATT GCG GCA TCA AAT ACG GGG GAA CTG GAT GCC CTG CAA CAG CTG GGA TTC TCC CTG GTA GAA GGT GAA GTT GAT TTG GCG CTA CCC GTG AAC AAT GTC AGT GAT AGC GGT GCT GTC GTG GCA CAA GAG ACC GAT ATT CCC GCA TTA CGT CAG TTA GCT AGC GCC GCA TTT GCG CAA AGC CGT TTT CGT GCG CCG TGG TAT GCG CCT GAC GCC AGC GGT CGC TTT TAT GCA CAG TGG ATT GAA AAT GCC GTG CGC GGC ACC TTT GAT CAT CAA TGT CTG ATT CTA CGT GCG GCG TCC GGC GAT ATT CGC GGC TAT GTC TCT TTA CGG GAA CTC AAT GCG ACA GAT GCG CGA ATT GGC CTG CTG GCT GGA CGC GGT GCA GGT GCT GAG CTG ATG CAA ACG GCG CTA AAC TGG GCG TAT GCT CGC GGT AAA ACA ACT TTG CGG GTG GCG ACC CAA ATG GGC AAC ACC GCC GCG CTT AAA CGA TAC ATA CAA AGT GGT GCG AAT GTA GAA AGC ACC GCG TAC TGG TTA TAC AGG 
CFT073                               GTG CAG GCC AAA ATT GCG GCA TCA AAT ACG GGT GAA CTG GAT GCC CTG CAA CAG CTG GGA TTC TCC CTG GTA GAA GGT GAA GTT GAT TTG GCG CTA CCC GTG AAC AAT GTC AGT GAT AGC GGT GCT GTA GTG GCA CAA GAG ACC GAT ATT CCC GCA TTA CGT CAG TTA GCC AGC GCC GCA TTT GCG CAA AGC CGT TTT CGT GCG CCA TGG TAT GCG CCT GAC GCC AGC GGT CGC TTT TAT GCG CAG TGG ATT GAA AAT GCC GTG CGC GGC ACC TTT GAT CAT CAA TGT CTG ATT TTA CGT GCG GCG TCC GGC GAT ATT CGC GGC TAT GTC TCT TTA CGG GAA CTC AAT GCG ACA GAT GCG CGA ATT GGC CTG CTG GCT GGA CGC GGT GCA GGT GCT GAG CTG ATG CAA ACA GCG CTA AAC TGG GCG TAT GCT CGC GGT AAA ACA ACT TTG CGG GTG GCG ACC CAG ATG GGC AAC ACC GCC GCG CTT AAA CGA TAC ATA CAA AGT GGT GCG AAT GTA GAA AGC ACC GCG TAC TGG TTA TAC AGG 
O157                                 GTG CAG GCC AAA ATT GCG GCA TCA AAT ACG GGG GAA CTG GAT GCC CTG CAA CAG CTG GGA TTC TCC CTG GTA GAA GGT GAA GTT GAT TTG GCG CTA CCC GTG AAC AAT GCC AGT GAT AGC GGT GCT GTA GTG GCA CAA GAG ACC GAT ATT CCC GCA TTA CGT CAG TTA GCC AGC GCC GCA TTT GCG CAA AGC CGT TTT CGT GCG CCG TGG TAT GCG CCT GAC GCC AGC AGT CGC TTT TAT GCA CAG TGG ATT GAA AAT GCC GTG CGC GGC ACC TTT GAT CAT CAA TGT CTG ATT TTA CGT GCG GCG TCC GGC GAT ATT CGC GGT TAT GTC TCT TTA CGG GAA CTC AAT GCT ACA GAT GCG CGA ATT GGC CTG CTG GCT GGA CGC GGT GCA GGT GCT GAG CTG ATG CAA ACG GCG CTA AAC TGG GCG TAT GCT CGC GGT AAA ACA ACT TTG CGG GTG GCG ACC CAA ATG GGC AAC ACC GCC GCG CTT AAA CGA TAC ATA CAA AGT GGT GCG AAT GTA GAA AGC ACC GCG TAC TGG TTA TAC AGG 
EDL933                               GTG CAG GCC AAA ATT GCG GCA TCA AAT ACG GGG GAA CTG GAT GCC CTG CAA CAG CTG GGA TTC TCC CTG GTA GAA GGT GAA GTT GAT TTG GCG CTA CCC GTG AAC AAT GCC AGT GAT AGC GGT GCT GTA GTG GCA CAA GAG ACC GAT ATT CCC GCA TTA CGT CAG TTA GCC AGC GCC GCA TTT GCG CAA AGC CGT TTT CGT GCG CCG TGG TAT GCG CCT GAC GCC AGC AGT CGC TTT TAT GCA CAG TGG ATT GAA AAT GCC GTG CGC GGC ACC TTT GAT CAT CAA TGT CTG ATT TTA CGT GCG GCG TCC GGC GAT ATT CGC GGT TAT GTC TCT TTA CGG GAA CTC AAT GCT ACA GAT GCG CGA ATT GGC CTG CTG GCT GGA CGC GGT GCA GGT GCT GAG CTG ATG CAA ACG GCG CTA AAC TGG GCG TAT GCT CGC GGT AAA ACA ACT TTG CGG GTG GCG ACC CAA ATG GGC AAC ACC GCC GCG CTT AAA CGA TAC ATA CAA AGT GGT GCG AAT GTA GAA AGC ACC GCG TAC TGG TTA TAC AGG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3790.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 181
# site patterns = 64
    5    4    6    3    6   14    5    1    5    1    1    6    8    7    6
    2    1    2    2    6    1    2    2    2    3    1    2    5    4    1
    2    5    4    4    1    4    1    4    4    1    1    1    5    1    4
    1    1    1    1    1    1    2    1    1    2    2    2    1    1    1
    1    3    1    1

1       
K12                   GTG CAG GCC AAA ATT GCG GCA TCA AAT ACG GGT GAA CTG GAT CAA GGA TTC TCC GTA GGT GTT TTG CTA CCC AAC GCC AGT AGC GCT GTA GAG ACC TTA CGT GCC TTT CCG TGG TAT CCT GAC AGT CGC GCA GGC CAT TGT TTA GGC GTC TCT CGG CTC GCG ACA CGA ATG ACG ACT CAA CTT TAC ATA AGG 
S2457T                ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ..C ... ... ... ... ..T ... ... ... ... ... ... G.. ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ..C ... ... ... ... ..T ... ... ... ... ... ... G.. ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... G.. ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ..G ... ... ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  4  4  4  4  4  4 | Ser TCT  1  1  1  1  1  1 | Tyr TAT  4  4  4  4  4  4 | Cys TGT  1  1  1  1  1  1
    TTC  1  1  1  1  1  1 |     TCC  2  2  2  2  2  2 |     TAC  3  3  3  3  3  3 |     TGC  0  0  0  0  0  0
Leu TTA  5  4  4  5  5  5 |     TCA  1  1  1  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  2  2  2  2  2  2 |     TCG  0  0  0  0  0  0 |     TAG  0  0  0  0  0  0 | Trp TGG  4  4  4  4  4  4
--------------------------------------------------------------------------------------------------------------
Leu CTT  1  1  1  1  1  1 | Pro CCT  1  1  1  1  1  1 | His CAT  1  1  1  1  1  1 | Arg CGT  4  4  4  4  4  4
    CTC  1  1  1  1  1  1 |     CCC  2  2  2  2  2  2 |     CAC  0  0  0  0  0  0 |     CGC  5  5  5  5  5  5
    CTA  2  3  3  2  2  2 |     CCA  0  0  0  1  0  0 | Gln CAA  7  7  7  6  7  7 |     CGA  2  2  2  2  2  2
    CTG  8  8  8  8  8  8 |     CCG  1  1  1  0  1  1 |     CAG  4  4  4  5  4  4 |     CGG  2  2  2  2  2  2
--------------------------------------------------------------------------------------------------------------
Ile ATT  6  6  6  6  6  6 | Thr ACT  1  1  1  1  1  1 | Asn AAT  5  5  5  5  5  5 | Ser AGT  3  2  2  2  3  3
    ATC  0  0  0  0  0  0 |     ACC  5  5  5  5  5  5 |     AAC  3  3  3  3  3  3 |     AGC  5  5  5  5  5  5
    ATA  1  1  1  1  1  1 |     ACA  2  2  2  3  2  2 | Lys AAA  3  3  3  3  3  3 | Arg AGA  0  0  0  0  0  0
Met ATG  2  2  2  2  2  2 |     ACG  2  2  2  1  2  2 |     AAG  0  0  0  0  0  0 |     AGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------
Val GTT  1  1  1  1  1  1 | Ala GCT  4  5  5  4  5  5 | Asp GAT  7  7  7  7  7  7 | Gly GGT  7  7  7  8  7  7
    GTC  1  3  3  2  1  1 |     GCC  8  6  6  7  8  8 |     GAC  1  1  1  1  1  1 |     GGC  5  5  5  5  4  4
    GTA  3  2  2  3  3  3 |     GCA  6  6  6  5  6  6 | Glu GAA  6  6  6  6  6  6 |     GGA  2  2  2  2  2  2
    GTG  5  5  5  5  5  5 |     GCG 15 15 15 16 14 14 |     GAG  2  2  2  2  2  2 |     GGG  0  1  1  0  1  1
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.15470    C:0.22652    A:0.21547    G:0.40331
position  2:    T:0.23757    C:0.28177    A:0.25414    G:0.22652
position  3:    T:0.28177    C:0.23204    A:0.22099    G:0.26519

#2: S2457T         
position  1:    T:0.14917    C:0.23204    A:0.20994    G:0.40884
position  2:    T:0.24309    C:0.27624    A:0.25414    G:0.22652
position  3:    T:0.28177    C:0.23204    A:0.21547    G:0.27072

#3: Shig4337       
position  1:    T:0.14917    C:0.23204    A:0.20994    G:0.40884
position  2:    T:0.24309    C:0.27624    A:0.25414    G:0.22652
position  3:    T:0.28177    C:0.23204    A:0.21547    G:0.27072

#4: CFT073         
position  1:    T:0.15470    C:0.22652    A:0.20994    G:0.40884
position  2:    T:0.24309    C:0.27624    A:0.25414    G:0.22652
position  3:    T:0.28177    C:0.23204    A:0.22099    G:0.26519

#5: O157           
position  1:    T:0.15470    C:0.22652    A:0.21547    G:0.40331
position  2:    T:0.23757    C:0.28177    A:0.25414    G:0.22652
position  3:    T:0.28729    C:0.22652    A:0.22099    G:0.26519

#6: EDL933         
position  1:    T:0.15470    C:0.22652    A:0.21547    G:0.40331
position  2:    T:0.23757    C:0.28177    A:0.25414    G:0.22652
position  3:    T:0.28729    C:0.22652    A:0.22099    G:0.26519

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      24 | Ser S TCT       6 | Tyr Y TAT      24 | Cys C TGT       6
      TTC       6 |       TCC      12 |       TAC      18 |       TGC       0
Leu L TTA      28 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG      12 |       TCG       0 |       TAG       0 | Trp W TGG      24
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       6 | His H CAT       6 | Arg R CGT      24
      CTC       6 |       CCC      12 |       CAC       0 |       CGC      30
      CTA      14 |       CCA       1 | Gln Q CAA      41 |       CGA      12
      CTG      48 |       CCG       5 |       CAG      25 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      36 | Thr T ACT       6 | Asn N AAT      30 | Ser S AGT      15
      ATC       0 |       ACC      30 |       AAC      18 |       AGC      30
      ATA       6 |       ACA      13 | Lys K AAA      18 | Arg R AGA       0
Met M ATG      12 |       ACG      11 |       AAG       0 |       AGG       6
------------------------------------------------------------------------------
Val V GTT       6 | Ala A GCT      28 | Asp D GAT      42 | Gly G GGT      43
      GTC      11 |       GCC      43 |       GAC       6 |       GGC      28
      GTA      16 |       GCA      35 | Glu E GAA      36 |       GGA      12
      GTG      30 |       GCG      89 |       GAG      12 |       GGG       4
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15285    C:0.22836    A:0.21271    G:0.40608
position  2:    T:0.24033    C:0.27901    A:0.25414    G:0.22652
position  3:    T:0.28361    C:0.23020    A:0.21915    G:0.26703

Codon frequencies under model, for use in evolver:
  0.01070195  0.00868664  0.00826969  0.01007651
  0.01242410  0.01008449  0.00960044  0.01169801
  0.01131700  0.00918588  0.00000000  0.00000000
  0.01008689  0.00818741  0.00000000  0.00949740
  0.01598845  0.01297764  0.01235471  0.01505406
  0.01856130  0.01506599  0.01434282  0.01747655
  0.01690732  0.01372348  0.01306475  0.01591923
  0.01506957  0.01223180  0.01164467  0.01418888
  0.01489247  0.01208804  0.01150781  0.01402213
  0.01728895  0.01403324  0.01335965  0.01627856
  0.01574835  0.01278276  0.01216918  0.01482800
  0.01403658  0.01139333  0.01084645  0.01321626
  0.02843107  0.02307717  0.02196946  0.02676952
  0.03300619  0.02679074  0.02550478  0.03107725
  0.03006504  0.02440344  0.02323208  0.02830799
  0.02679710  0.02175089  0.02070685  0.02523104



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               0.1721 (0.0050 0.0290)
Shig4337             0.1721 (0.0050 0.0290)-1.0000 (0.0000 0.0000)
CFT073               0.1717 (0.0050 0.0290) 0.0000 (0.0000 0.0590) 0.0000 (0.0000 0.0590)
O157                 0.0000 (0.0000 0.0217) 0.1370 (0.0050 0.0364) 0.1370 (0.0050 0.0364) 0.0966 (0.0050 0.0516)
EDL933               0.0000 (0.0000 0.0217) 0.1370 (0.0050 0.0364) 0.1370 (0.0050 0.0364) 0.0966 (0.0050 0.0516)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 15
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -814.351111     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.00000  0.03471  0.00000  0.00000  0.00000  0.03443  0.01696  0.00000  0.00000  4.13825  0.98545  0.00000  0.00000 12.85171
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.08612

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.034707): 0.000000, (4: 0.034431, (5: 0.000004, 6: 0.000004): 0.016960): 0.000000);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.034707): 0.000000, (CFT073: 0.034431, (O157: 0.000004, EDL933: 0.000004): 0.016960): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  4.13825


dN/dS for site classes (K=3)

p:   0.98545  0.00000  0.01455
w:   0.00000  1.00000 12.85171

dN & dS for each branch

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

   7..8       0.000    173.4    369.6   0.1869   0.0000   0.0000    0.0    0.0
   8..1       0.000    173.4    369.6   0.1869   0.0000   0.0000    0.0    0.0
   8..9       0.035    173.4    369.6   0.1869   0.0048   0.0259    4.5    1.8
   9..2       0.000    173.4    369.6   0.1869   0.0000   0.0000    0.0    0.0
   9..3       0.000    173.4    369.6   0.1869   0.0000   0.0000    0.0    0.0
   7..10      0.000    173.4    369.6   0.1869   0.0000   0.0000    0.0    0.0
  10..4       0.034    173.4    369.6   0.1869   0.0048   0.0257    4.5    1.8
  10..11      0.017    173.4    369.6   0.1869   0.0024   0.0127    2.2    0.9
  11..5       0.000    173.4    369.6   0.1869   0.0000   0.0000    0.0    0.0
  11..6       0.000    173.4    369.6   0.1869   0.0000   0.0000    0.0    0.0


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

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

    37 A      1.000**       12.852
    77 S      1.000**       12.852


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

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

    37 A      0.882         5.757 +- 3.034
    77 S      0.874         5.711 +- 3.056



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:   0.866  0.115  0.017  0.003  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.071  0.084  0.099  0.110  0.115  0.114  0.111  0.105  0.099  0.092

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.024
 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 0.003 0.016 0.133
 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 0.004 0.015 0.087 0.707

sum of density on p0-p1 =   1.000000
