
seed used = 140009241

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2433.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 149
# site patterns = 68
    1    1    1    2    2    1    2    1    2    3    4    9    2    1    2
   14    2    4    2    5    2    2    8    3    6    2    2    2    2    6
    3    1    1    1    1    5    3    1    1    1    1    2    1    1    1
    2    2    1    1    1    1    1    1    1    2    1    1    1    3    1
    1    2    1    1    1    1    1    1

1       
K12                   ATG AAG AGT ACT GAG TTT CAT CCT GTC TAT GAT GCG CAC GGT CGC CTG CGT TTA CCC TTG CTC TTC TGG CTT GTG CTA CAG CGA ACC TTT ATT GCC GGT TCG CGC GGT AAT GGG CTG CCT GGC CCG GCG TTG AGC CGG GCT ACG CCT CGC ACC CGT GTA CAG GTT TGC CAA AAC GAA TCC AGC ATC GTA ATT TGT TAT GTA AAA 
S2457T                ... ... ... ... ... ..C ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..C ..T ... ... ... ... ... ... T.. ... ... ... .A. ..G ... ... ... ... ... ... ... ... ... ... ... ... A.. .A. ... 
Shig4337              ... ... ... ... ... ..C ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..C ..T ... ... ... ... ... ... T.. ... ... ... .A. ..G ... ... ... ... ... ... ... ... ... ... ... ... A.. .A. ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... T.. ..C ..T ... ..A C.. ..T ... ... T.A ..C ..T .T. .A. ..G ..A ... ..T ... ... ... ... ... ... ... ..C ... A.. .A. ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... 

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

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

#1: K12            
position  1:    T:0.23490    C:0.32215    A:0.14765    G:0.29530
position  2:    T:0.40940    C:0.18792    A:0.18121    G:0.22148
position  3:    T:0.32215    C:0.17450    A:0.10738    G:0.39597

#2: S2457T         
position  1:    T:0.23490    C:0.32215    A:0.14765    G:0.29530
position  2:    T:0.40268    C:0.18792    A:0.19463    G:0.21477
position  3:    T:0.31544    C:0.17450    A:0.10738    G:0.40268

#3: Shig4337       
position  1:    T:0.23490    C:0.32215    A:0.14765    G:0.29530
position  2:    T:0.40268    C:0.18792    A:0.19463    G:0.21477
position  3:    T:0.31544    C:0.17450    A:0.10738    G:0.40268

#4: CFT073         
position  1:    T:0.23490    C:0.32215    A:0.14765    G:0.29530
position  2:    T:0.40940    C:0.18121    A:0.19463    G:0.21477
position  3:    T:0.32215    C:0.16779    A:0.12752    G:0.38255

#5: O157           
position  1:    T:0.22819    C:0.32215    A:0.15436    G:0.29530
position  2:    T:0.40940    C:0.18792    A:0.18121    G:0.22148
position  3:    T:0.32215    C:0.17450    A:0.10738    G:0.39597

#6: EDL933         
position  1:    T:0.22819    C:0.32215    A:0.15436    G:0.29530
position  2:    T:0.40940    C:0.18792    A:0.18121    G:0.22148
position  3:    T:0.32215    C:0.17450    A:0.10738    G:0.39597

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      40 | Ser S TCT       0 | Tyr Y TAT      19 | Cys C TGT       7
      TTC      14 |       TCC       6 |       TAC       0 |       TGC       5
Leu L TTA      24 |       TCA       1 | *** * TAA       0 | *** * TGA       0
      TTG      36 |       TCG       8 |       TAG       0 | Trp W TGG      48
------------------------------------------------------------------------------
Leu L CTT      18 | Pro P CCT      14 | His H CAT      15 | Arg R CGT      18
      CTC      12 |       CCC      16 |       CAC      12 |       CGC      21
      CTA      12 |       CCA       0 | Gln Q CAA       7 |       CGA      12
      CTG      90 |       CCG      12 |       CAG      17 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      23 | Thr T ACT      12 | Asn N AAT      23 | Ser S AGT       7
      ATC      14 |       ACC      17 |       AAC       6 |       AGC      11
      ATA       0 |       ACA       0 | Lys K AAA       6 | Arg R AGA       0
Met M ATG       6 |       ACG       3 |       AAG       6 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      12 | Ala A GCT      12 | Asp D GAT      24 | Gly G GGT      42
      GTC      12 |       GCC       6 |       GAC       0 |       GGC       3
      GTA      12 |       GCA       1 | Glu E GAA      21 |       GGA       3
      GTG      39 |       GCG      59 |       GAG      12 |       GGG       6
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.23266    C:0.32215    A:0.14989    G:0.29530
position  2:    T:0.40716    C:0.18680    A:0.18792    G:0.21812
position  3:    T:0.31991    C:0.17338    A:0.11074    G:0.39597

Codon frequencies under model, for use in evolver:
  0.03117102  0.01689338  0.01078997  0.03858231
  0.01430099  0.00775054  0.00495034  0.01770123
  0.01438662  0.00779695  0.00000000  0.00000000
  0.01669876  0.00905003  0.00000000  0.02066910
  0.04315987  0.02339084  0.01493996  0.05342166
  0.01980137  0.01073151  0.00685432  0.02450939
  0.01991994  0.01079577  0.00689536  0.02465615
  0.02312136  0.01253081  0.00800355  0.02861875
  0.02008133  0.01088324  0.00695123  0.02485591
  0.00921314  0.00499313  0.00318916  0.01140367
  0.00926831  0.00502303  0.00320826  0.01147196
  0.01075786  0.00583031  0.00372387  0.01331567
  0.03956322  0.02144160  0.01369496  0.04896986
  0.01815126  0.00983722  0.00628313  0.02246694
  0.01825995  0.00989612  0.00632075  0.02260147
  0.02119458  0.01148657  0.00733659  0.02623385



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               0.2341 (0.0123 0.0524)
Shig4337             0.2341 (0.0123 0.0524)-1.0000 (0.0000 0.0000)
CFT073               0.1194 (0.0154 0.1287) 0.0235 (0.0030 0.1295) 0.0235 (0.0030 0.1295)
O157                -1.0000 (0.0031 0.0000) 0.1750 (0.0092 0.0525) 0.1750 (0.0092 0.0525) 0.0952 (0.0123 0.1288)
EDL933              -1.0000 (0.0031 0.0000) 0.1750 (0.0092 0.0525) 0.1750 (0.0092 0.0525) 0.0952 (0.0123 0.1288)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 27
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 10  np: 15):   -720.435005     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.00743  0.07308  0.00000  0.00000  0.00000  0.16341  0.00000  0.00000  0.00000  5.43039  0.95937  0.00000  0.00000  8.91171
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.24393

((1: 0.007427, (2: 0.000004, 3: 0.000004): 0.073079): 0.000000, (4: 0.163410, (5: 0.000004, 6: 0.000004): 0.000000): 0.000000);

((K12: 0.007427, (S2457T: 0.000004, Shig4337: 0.000004): 0.073079): 0.000000, (CFT073: 0.163410, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  5.43039


dN/dS for site classes (K=3)

p:   0.95937  0.00000  0.04063
w:   0.00000  1.00000  8.91171

dN & dS for each branch

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

   7..8       0.000    142.7    304.3   0.3621   0.0000   0.0000    0.0    0.0
   8..1       0.007    142.7    304.3   0.3621   0.0016   0.0044    0.6    0.5
   8..9       0.073    142.7    304.3   0.3621   0.0156   0.0431    6.1    4.7
   9..2       0.000    142.7    304.3   0.3621   0.0000   0.0000    0.0    0.0
   9..3       0.000    142.7    304.3   0.3621   0.0000   0.0000    0.0    0.0
   7..10      0.000    142.7    304.3   0.3621   0.0000   0.0000    0.0    0.0
  10..4       0.163    142.7    304.3   0.3621   0.0349   0.0963   13.7   10.6
  10..11      0.000    142.7    304.3   0.3621   0.0000   0.0000    0.0    0.0
  11..5       0.000    142.7    304.3   0.3621   0.0000   0.0000    0.0    0.0
  11..6       0.000    142.7    304.3   0.3621   0.0000   0.0000    0.0    0.0


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

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

    83 T      1.000**       8.912
    87 T      1.000**       8.912
    89 R      1.000**       8.912
   145 Y      1.000**       8.912
   147 V      1.000**       8.912


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

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

    83 T      0.920         7.149 +- 2.831
    89 R      0.857         6.692 +- 3.154
   147 V      0.947         7.323 +- 2.663



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:   0.939  0.058  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.013  0.026  0.046  0.070  0.096  0.119  0.138  0.154  0.165  0.173

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 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 0.009 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 0.007 0.111 0.756

sum of density on p0-p1 =   1.000000
