
seed used = 140031285

K12                                  ATG AAA ATT AAA ACT CTG GCA ATC GTT GTT CTG TCG GCT CTG TCC CTC AGT TCT ACA GCG GCT CTG GCC GCT GCC ACG ACG GTT AAT GGT GGG ACC GTT CAC TTT AAA GGG GAA GTT GTT AAC GCC GCT TGC GCA GTT GAT GCA GGC TCT GTT GAT CAA ACC GTT CAG TTA GGA CAG GTT CGT ACC GCA TCG CTG GCA CAG GAA GGA GCA ACC AGT TCT GCT GTC GGT TTT AAC ATT CAG CTG AAT GAT TGC GAT ACC AAT GTT GCA TCT AAA GCC GCT GTT GCC TTT TTA GGT ACG GCG ATT GAT GCG GGT CAT ACC AAC GTT CTG GCT CTG CAG AGT TCA GCT GCG GGT AGC GCA ACA AAC GTT GGT GTG CAG ATC CTG GAC AGA ACG GGT GCT GCG CTG ACG CTG GAT GGT GCG ACA TTT AGT TCA GAA ACA ACC CTG AAT AAC GGA ACC AAT ACC ATT CCG TTC CAG GCG CGT TAT TTT GCA ACC GGG GCC GCA ACC CCG GGT GCT GCT AAT GCG GAT GCG ACC TTC AAG GTT CAG TAT CAA 
S2457T                               ATG AAA ATT AAA ACT CTG GCA ATC GTT GTT CTG TCG GCT CTG TCC CTC AGT TCC GCA GCG GCT CTG GCC GAT ACT ACG ACG GTA AAT GGT GGG ACC ATT CAC TTT AAA GGG GAA GTT GTT AAC GCC GCT TGC GCA GTT GAT GCA GGC TCT GTT GAT CAA ACC GTT CAG TTG GGA CAG GTT CGT ACC GCT AGC CTG AAG CAG GCT GGA GCA ACC AGC TCT GCC GTT GGT TTT AAC ATT CAG CTG AAT GAT TGC GAT ACC ACT GTT GCC ACA AAA GCC GCT GTT GCC TTC TTA GGT ACG GCA ATT GAT GCT ACG CGT ACT GAT GTA CTG GCT CTG CAG AGT TCT GCT GCA GGT AGT GCA ACA AAC GTT GGC GTG CAG ATC CTA GAC AGA ACA GGC AAT GCT CTG ACG CTG GAC GGT GCG ACA TTT AGT GCA CAA ACA ACC CTG AAT AAC GGT ACC AAC ACC ATT CCG TTC CAG GCG CGT TAT TAT GCA ATC GGC GAG GCA ACC CCG GGT GCA GCT AAT GCG GAT GCA ACC TTC AAG GTT CAG TAT CAA 
Shig4337                             ATG AAA ATT AAA ACT CTG GCA ATC GTT GTT CTG TCG GCT CTG TCC CTC AGT TCC GCA GCG GCT CTG GCC GAT ACT ACG ACG GTA AAT GGT GGG ACC ATT CAC TTT AAA GGG GAA GTT GTT AAC GCC GCT TGC GCA GTT GAT GCA GGC TCT GTT GAT CAA ACC GTT CAG TTG GGA CAG GTT CGT ACC GCT AGC CTG AAG CAG GCT GGA GCA ACC AGC TCT GCC GTT GGT TTT AAC ATT CAG CTG AAT GAT TGC GAT ACC ACT GTT GCC ACA AAA GCC GCT GTT GCC TTC TTA GGT ACG GCA ATT GAT GCT ACG CGT ACT GAT GTA CTG GCT CTG CAG AGT TCT GCT GCA GGT AGT GCA ACA AAC GTT GGC GTG CAG ATC CTA GAC AGA ACA GGC AAT GCT CTG ACG CTG GAC GGT GCG ACA TTT AGT GCA CAA ACA ACC CTG AAT AAC GGT ACC AAC ACC ATT CCG TTC CAG GCG CGT TAT TAT GCA ATC GGC GAG GCA ACC CCG GGT GCA GCT AAT GCG GAT GCA ACC TTC AAG GTT CAG TAT CAA 
CFT073                               ATG AAA ATT AAA ACT CTG GCA ATC GTT GTT CTG TCG GCT CTG TCC CTC AGT TCC ACA GCG GCT CTG GCC GCT GCC ACG ACG GTT AAT GGT GGG ACC GTT CAC TTT AAA GGG GAA GTT GTT AAC GCC GCT TGC GCA GTT GAT GCA GGC TCT GTT GAT CAA ACC GTT CAG TTA GGA CAG GTT CGT ACC GCA TCG CTG GAC CAG GAT GGA GCG ACC AGC TCT GCT GTC GGT TTT AAC ATT CAA CTG AAT GAT TGC GAT ACC GAT GTT GCA AGT AAA GCT GCT GTT GCC TTC TTA GGT ACA ACA ATT GAC ACG AAT CAT ACC AAC GTA CTG GCT CTG CAA AGT TCT GCT GCG GGT AGC GCA ACA AAC GTT GGT GTG CAG ATC CTG GAT AAA ACA GGG ACT GCG TTG GCT TTG GAT GGT GCG TCA TTT AGT GCA CAA ACC ACC CTG AAT AAC GGA ACC AAC ACC ATT CCG TTC CAG GCG CGT TAT TAT GCC ATT GGT GCC GCA ACC CCT GGC GCA GCT AAT GCG GAT GCG ACC TTC AAG GTT CAG TAT CAA 
O157                                 ATG AAA ATT AAA ACT CTG GCA ATC GTT GTT CTG TCG GCT CTG TCC CTC AGT TCT ACA GCG GCT CTG GCC GCT GCC ACG ACG GTT AAT GGT GGG ACC GTT CAC TTT AAA GGG GAA GTT GTT AAC GCC GCT TGC GCA GTT GAT GCA GGC TCT GTT GAT CAA ACC GTT CAG TTA GGA CAG GTT CGT ACC GCA TCG CTG GCA CAG GAC GGA GCA ACC AGT TCT GCT GTC GGT TTT AAC ATT CAG CTG AAT GAT TGC GAT ACC AAT GTT GCA TCT AAA GCC GCT GTT GCC TTT TTA GGT ACG GTG ATT GAT GCG GGT CAT ACC AAC GTT CTG GCT CTG CAG AGT TCA GCT GCG GGT AGC GCA ACA AAC GTT GGT GTG CAG ATC CTG GAC AGA ACG GGT GCT GCG CTG ACG CTG GAT GGT GCG ACA TTC AGT GAG CAA ACA ACC CTG AAT AAC GGT ACT AAC ACC ATT CCG TTC CAG GCG CGT TAT TAT GCA ATC GGC GAG GCA ACC CCG GGT GCT GCT AAT GCG GAT GCG ACC TTC AAG GTT CAG TAT CAA 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4314.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 182
# site patterns = 99
    1    4    4    1    9    5    2   12    1    7    1    1    3    1    1
    4    3    1    1    2    1    4    5    2    9    1    1    2    1    4
    2    5    1    2    2    6    1    2    2    1    1    1    1    1    1
    1    1    2    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
    1    2    1    1    1    1    1    1    1    1    1    1    1    2    2
    1    1    1    1    1    1    1    1    1

1       
K12                   ATG AAA ATT ACT CTG GCA ATC GTT TCG GCT TCC CTC AGT TCT ACA GCG GCC GCT GCC ACG GTT AAT GGT GGG ACC GTT CAC TTT GAA AAC TGC GAT GGC TCT CAA CAG TTA GGA CGT GCA TCG GCA GAA GCA AGT GCT GTC CAG AAT GCA TCT GCC TTT TTA ACG GCG GAT GCG GGT CAT ACC AAC GTT TCA GCG AGC ACA GGT GTG CTG GAC AGA ACG GGT GCT GCG CTG ACG GAT ACA TTT TCA GAA ACA GGA ACC AAT CCG TTC TAT TTT GCA ACC GGG GCC CCG GGT GCT AAG 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ..C G.. ... ... .A. A.T ... ..A ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ..G ... ... ..T AGC AAG .CT ... ..C ..C ..T ... .C. ..C A.A ... ..C ... ... ..A ... ..T ACG .G. ..T G.T ..A ..T ..A ..T ... ..C ... ..A ... ... ..A ..C AA. ..T ... ... ..C ... ... G.. C.. ... ..T ... ..C ... ... ... .A. ... .T. ..C .AG ... ... ..A ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ..C G.. ... ... .A. A.T ... ..A ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ..G ... ... ..T AGC AAG .CT ... ..C ..C ..T ... .C. ..C A.A ... ..C ... ... ..A ... ..T ACG .G. ..T G.T ..A ..T ..A ..T ... ..C ... ..A ... ... ..A ..C AA. ..T ... ... ..C ... ... G.. C.. ... ..T ... ..C ... ... ... .A. ... .T. ..C .AG ... ... ..A ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC ..T ..G ..C ... ... ..A G.. ... AG. ..T ..C ... ..A A.A ..C A.. AA. ... ... ... ..A ..T ... ... ... ... ... ... ..T .A. ..A ..G A.. ... T.. G.T ... T.. ... G.. C.. ..C ... ... ..C ... ... ... .A. ..C .TT ..T ... ..T ..C ..A ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C GAG C.. ... ..T ..T ..C ... ... ... .A. ... .T. ..C .AG ... ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  5  3  3  3  3 | Ser TCT  4  3  3  3  4 | Tyr TAT  2  3  3  3  3 | Cys TGT  0  0  0  0  0
    TTC  2  3  3  3  3 |     TCC  1  2  2  2  1 |     TAC  0  0  0  0  0 |     TGC  2  2  2  2  2
Leu TTA  2  1  1  2  2 |     TCA  2  0  0  1  1 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  0  1  1  2  0 |     TCG  2  1  1  2  2 |     TAG  0  0  0  0  0 | Trp TGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Leu CTT  0  0  0  0  0 | Pro CCT  0  0  0  1  0 | His CAT  1  0  0  1  1 | Arg CGT  2  3  3  2  2
    CTC  1  1  1  1  1 |     CCC  0  0  0  0  0 |     CAC  1  1  1  1  1 |     CGC  0  0  0  0  0
    CTA  0  1  1  0  0 |     CCA  0  0  0  0  0 | Gln CAA  2  3  3  5  3 |     CGA  0  0  0  0  0
    CTG 12 11 11 10 12 |     CCG  2  2  2  1  2 |     CAG  8  8  8  6  8 |     CGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Ile ATT  4  5  5  5  4 | Thr ACT  1  4  4  2  2 | Asn AAT  6  5  5  5  5 | Ser AGT  4  4  4  4  4
    ATC  2  3  3  2  3 |     ACC 12 10 10 12 10 |     AAC  5  5  5  6  6 |     AGC  1  2  2  2  1
    ATA  0  0  0  0  0 |     ACA  4  5  5  5  4 | Lys AAA  4  4  4  5  4 | Arg AGA  1  1  1  0  1
Met ATG  1  1  1  1  1 |     ACG  5  5  5  3  5 |     AAG  1  2  2  1  1 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT 15 13 13 14 15 | Ala GCT 11 11 11 11 11 | Asp GAT  7  8  8  9  7 | Gly GGT  9  7  7  7 10
    GTC  1  0  0  1  1 |     GCC  6  6  6  6  5 |     GAC  1  2  2  2  2 |     GGC  1  4  4  2  2
    GTA  0  2  2  1  0 |     GCA 10 13 13  9 10 | Glu GAA  3  1  1  1  1 |     GGA  3  2  2  3  2
    GTG  1  1  1  1  2 |     GCG  9  4  4  8  8 |     GAG  0  1  1  0  2 |     GGG  3  2  2  3  2
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.12088    C:0.15934    A:0.28022    G:0.43956
position  2:    T:0.25275    C:0.37912    A:0.22527    G:0.14286
position  3:    T:0.39011    C:0.19780    A:0.17033    G:0.24176

#2: S2457T         
position  1:    T:0.10440    C:0.16484    A:0.30769    G:0.42308
position  2:    T:0.25275    C:0.36264    A:0.23626    G:0.14835
position  3:    T:0.37912    C:0.22527    A:0.18132    G:0.21429

#3: Shig4337       
position  1:    T:0.10440    C:0.16484    A:0.30769    G:0.42308
position  2:    T:0.25275    C:0.36264    A:0.23626    G:0.14835
position  3:    T:0.37912    C:0.22527    A:0.18132    G:0.21429

#4: CFT073         
position  1:    T:0.12637    C:0.15385    A:0.29121    G:0.42857
position  2:    T:0.25275    C:0.36264    A:0.24725    G:0.13736
position  3:    T:0.38462    C:0.23077    A:0.17582    G:0.20879

#5: O157           
position  1:    T:0.11538    C:0.16484    A:0.28022    G:0.43956
position  2:    T:0.25824    C:0.35714    A:0.24176    G:0.14286
position  3:    T:0.39011    C:0.20879    A:0.15385    G:0.24725

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      17 | Ser S TCT      17 | Tyr Y TAT      14 | Cys C TGT       0
      TTC      14 |       TCC       8 |       TAC       0 |       TGC      10
Leu L TTA       8 |       TCA       4 | *** * TAA       0 | *** * TGA       0
      TTG       4 |       TCG       8 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       1 | His H CAT       3 | Arg R CGT      12
      CTC       5 |       CCC       0 |       CAC       5 |       CGC       0
      CTA       2 |       CCA       0 | Gln Q CAA      16 |       CGA       0
      CTG      56 |       CCG       9 |       CAG      38 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      23 | Thr T ACT      13 | Asn N AAT      26 | Ser S AGT      20
      ATC      13 |       ACC      54 |       AAC      27 |       AGC       8
      ATA       0 |       ACA      23 | Lys K AAA      21 | Arg R AGA       4
Met M ATG       5 |       ACG      23 |       AAG       7 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      70 | Ala A GCT      55 | Asp D GAT      39 | Gly G GGT      40
      GTC       3 |       GCC      29 |       GAC       9 |       GGC      13
      GTA       5 |       GCA      55 | Glu E GAA       7 |       GGA      12
      GTG       6 |       GCG      33 |       GAG       4 |       GGG      12
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.11429    C:0.16154    A:0.29341    G:0.43077
position  2:    T:0.25385    C:0.36484    A:0.23736    G:0.14396
position  3:    T:0.38462    C:0.21758    A:0.17253    G:0.22527

Codon frequencies under model, for use in evolver:
  0.01131226  0.00639950  0.00507435  0.00662575
  0.01625831  0.00919756  0.00729301  0.00952272
  0.01057769  0.00598395  0.00000000  0.00000000
  0.00641518  0.00362916  0.00000000  0.00375746
  0.01598944  0.00904545  0.00717240  0.00936524
  0.02298049  0.01300039  0.01030839  0.01346000
  0.01495116  0.00845809  0.00670666  0.00875711
  0.00906760  0.00512967  0.00406747  0.00531102
  0.02904204  0.01642950  0.01302743  0.01701034
  0.04174007  0.02361296  0.01872340  0.02444776
  0.02715619  0.01536265  0.01218149  0.01590577
  0.01646973  0.00931716  0.00738785  0.00964656
  0.04263850  0.02412121  0.01912641  0.02497398
  0.06128131  0.03466771  0.02748904  0.03589334
  0.03986977  0.02255490  0.01788444  0.02335229
  0.02418028  0.01367913  0.01084658  0.01416273



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               0.2303 (0.0619 0.2688)
Shig4337             0.2303 (0.0619 0.2688)-1.0000 (0.0000 0.0000)
CFT073               0.2187 (0.0452 0.2065) 0.2013 (0.0625 0.3104) 0.2013 (0.0625 0.3104)
O157                 0.4784 (0.0217 0.0453) 0.1883 (0.0509 0.2706) 0.1883 (0.0509 0.2706) 0.1674 (0.0415 0.2482)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 86
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1145.822809     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00000  0.05295  0.47155  0.00000  0.00000  0.00000  0.33592  0.04787  2.75179  0.87985  0.07067  0.05380  9.82081
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.90829

((1: 0.052947, (2: 0.000004, 3: 0.000004): 0.471545): 0.000000, (4: 0.335920, 5: 0.047872): 0.000000);

((K12: 0.052947, (S2457T: 0.000004, Shig4337: 0.000004): 0.471545): 0.000000, (CFT073: 0.335920, O157: 0.047872): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.75179


dN/dS for site classes (K=3)

p:   0.87985  0.07067  0.04949
w:   0.05380  1.00000  9.82081

dN & dS for each branch

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

   6..7       0.000    164.6    381.4   0.6040   0.0000   0.0000    0.0    0.0
   7..1       0.053    164.6    381.4   0.6040   0.0147   0.0244    4.0    5.6
   7..8       0.472    164.6    381.4   0.6040   0.1312   0.2173   35.8   50.1
   8..2       0.000    164.6    381.4   0.6040   0.0000   0.0000    0.0    0.0
   8..3       0.000    164.6    381.4   0.6040   0.0000   0.0000    0.0    0.0
   6..9       0.000    164.6    381.4   0.6040   0.0000   0.0000    0.0    0.0
   9..4       0.336    164.6    381.4   0.6040   0.0935   0.1548   25.5   35.7
   9..5       0.048    164.6    381.4   0.6040   0.0133   0.0221    3.6    5.1


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

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

    64 S      0.922         9.134
    66 A      0.985*        9.688
    68 E      0.760         7.687
    90 S      0.961*        9.476
   100 A      0.781         7.879
   104 G      0.972*        9.572
   132 A      0.640         6.641
   143 S      0.865         8.626
   165 A      0.966*        9.521


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

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

    64 S      0.901         7.179 +- 2.795
    66 A      0.975*        7.702 +- 2.240
    68 E      0.735         5.992 +- 3.494
    90 S      0.944         7.487 +- 2.498
   100 A      0.747         6.096 +- 3.467
   104 G      0.963*        7.609 +- 2.343
   132 A      0.667         5.443 +- 3.558
   143 S      0.817         6.625 +- 3.234
   165 A      0.946         7.511 +- 2.484



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:   0.968  0.032  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.007  0.028  0.062  0.101  0.133  0.156  0.168  0.173  0.172

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 0.009
 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 0.048 0.230
 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 0.024 0.533 0.154

sum of density on p0-p1 =   1.000000
