
seed used = 140006009

K12                                  ATG AAT CGT GAT TCC TTT TAT CCA GCC ATC GCC TGT TTT CCG CTG TTA CTG ATG CTG GCC GGG TGT GCG CCT ATG CAT GAA ACC CGC CAG GCG TTA AGC CAG CAA ACG CCC GCT GCA CAA GTT GAC ACC GCA TTA CCC ACG GCG CTG AAA ATG GTT GGC --- --- --- --- --- --- --- CAG ACA GCC AAT GGT GGC TGG AGT ATC ACG ATA ATC AAC TCA CTT CCT 
Shig4337                             ATG AAT CGT GAT TCC TTT TAT CCA GCC ATC GCC TGT TTT CCG CTG TTA CTG ATG CTG GCC GGG TGT GCG CCT ATG CAT GAA ACC CGC CAG GCG TTA AGC CAG CAA ACG CCC GCT GCA CAA GTT GAC ACC GCA TTA CCC ACG GCG CTG AAA AAT GGT TGG CCA GAC AGC CAA TGG TGG CTG GAG TAT CAC GAT AAT CAG CTC ACT TCA TTA ATT AAC AAT GCA CTA CAG 
CFT073                               ATG AAT CGT GAT TCT TTT TAT CCA GCC ATC GCC TGT TTT CCG CTG TTA CTG ATG CTG GCC GGG TGT GCG CCT ATG CAT GAA ACC CGC CAG GCG TTA AGC CAG CAA ACA CCC GCG GCA CAA GTT GAC ACC GCA TTA CCC ACG GCG CTG AAA AAT GGT TGG CCA GAC AGC CAA TGG TGG CTG GAG TAT CAC GAT AAT CAA CTC ACT TCC TTA ATT AAT AAC GCA CTA CAG 
O157                                 ATG AAT CGT GAT TCC TTT TAT CCA GCC ATC GCC TGT TTT CCG CTG TTA CTG ATG CTG GCC GGG TGT GCG CCT ATG CAT GAA ACC CGC CAG GCG TTA AGC CAG CAA ACG CCC GCT GCA CAA GTT GAC ACC GCA TTA CCC ACG GCG CTG AAA AAT GGT TGG CCA GAC AGC CAA TGG TGG CTG GAG TAT CAC GAT AAT CAA CTC ACT TCC TTA ATT AAC AAT GCA CTA CAG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2139.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 76
# site patterns = 57
    3    1    1    1    1    2    1    1    3    1    2    1    4    3    1
    3    1    1    1    2    1    2    1    2    1    2    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    1    1    1    1    1    1

K12                                  ATG AAT CGT GAT TCC TTT TAT CCA GCC ATC TGT CCG CTG TTA GGG GCG CCT CAT GAA ACC CGC CAG AGC CAA ACG CCC GCT GCA GTT GAC ACG AAA ATG GTT GGC --- --- --- --- --- --- CAG ACA GCC AAT GGT GGC TGG AGT ATC ACG ATA ATC AAC TCA CTT CCT 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AT .G. T.G CCA GAC AGC CAA TGG CTG G.. TAT CA. G.. AA. CAG CTC .C. TCA TTA ..T .A. ..T G.. ..A .AG 
CFT073                               ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ..G ... ... ... ... ... .AT .G. T.G CCA GAC AGC CAA TGG CTG G.. TAT CA. G.. AA. CAA CTC .C. TC. TTA ..T .AT ... G.. ..A .AG 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AT .G. T.G CCA GAC AGC CAA TGG CTG G.. TAT CA. G.. AA. CAA CTC .C. TC. TTA ..T .A. ..T G.. ..A .AG 



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

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

#1: K12            
position  1:    T:0.15942    C:0.27536    A:0.28986    G:0.27536
position  2:    T:0.28986    C:0.34783    A:0.20290    G:0.15942
position  3:    T:0.26087    C:0.26087    A:0.18841    G:0.28986

#2: Shig4337       
position  1:    T:0.19737    C:0.31579    A:0.23684    G:0.25000
position  2:    T:0.25000    C:0.30263    A:0.30263    G:0.14474
position  3:    T:0.26316    C:0.22368    A:0.21053    G:0.30263

#3: CFT073         
position  1:    T:0.19737    C:0.31579    A:0.23684    G:0.25000
position  2:    T:0.25000    C:0.30263    A:0.30263    G:0.14474
position  3:    T:0.26316    C:0.22368    A:0.22368    G:0.28947

#4: O157           
position  1:    T:0.19737    C:0.31579    A:0.23684    G:0.25000
position  2:    T:0.25000    C:0.30263    A:0.30263    G:0.14474
position  3:    T:0.26316    C:0.23684    A:0.21053    G:0.28947

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       8 | Ser S TCT       1 | Tyr Y TAT       7 | Cys C TGT       8
      TTC       0 |       TCC       5 |       TAC       0 |       TGC       0
Leu L TTA      15 |       TCA       2 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       0 |       TAG       0 | Trp W TGG      10
------------------------------------------------------------------------------
Leu L CTT       1 | Pro P CCT       5 | His H CAT       4 | Arg R CGT       4
      CTC       3 |       CCC       8 |       CAC       3 |       CGC       4
      CTA       3 |       CCA       7 | Gln Q CAA      13 |       CGA       0
      CTG      19 |       CCG       4 |       CAG      13 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       3 | Thr T ACT       3 | Asn N AAT      14 | Ser S AGT       1
      ATC       6 |       ACC       8 |       AAC       4 |       AGC       7
      ATA       1 |       ACA       2 | Lys K AAA       4 | Arg R AGA       0
Met M ATG      13 |       ACG       8 |       AAG       0 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       5 | Ala A GCT       3 | Asp D GAT       7 | Gly G GGT       4
      GTC       0 |       GCC      13 |       GAC       7 |       GGC       2
      GTA       0 |       GCA      11 | Glu E GAA       4 |       GGA       0
      GTG       0 |       GCG      13 |       GAG       3 |       GGG       4
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.18855    C:0.30640    A:0.24916    G:0.25589
position  2:    T:0.25926    C:0.31313    A:0.27946    G:0.14815
position  3:    T:0.26263    C:0.23569    A:0.20875    G:0.29293

Codon frequencies under model, for use in evolver:
  0.01326625  0.01190561  0.01054497  0.01479697
  0.01602288  0.01437950  0.01273613  0.01787167
  0.01429999  0.01283332  0.00000000  0.00000000
  0.00758072  0.00680321  0.00000000  0.00845541
  0.02155766  0.01934662  0.01713557  0.02404508
  0.02603717  0.02336669  0.02069621  0.02904146
  0.02323748  0.02085415  0.01847081  0.02591872
  0.01231866  0.01105521  0.00979176  0.01374005
  0.01753040  0.01573241  0.01393442  0.01955314
  0.02117309  0.01900149  0.01682989  0.02361613
  0.01889641  0.01695832  0.01502022  0.02107676
  0.01001737  0.00898995  0.00796253  0.01117322
  0.01800420  0.01615761  0.01431103  0.02008161
  0.02174533  0.01951504  0.01728475  0.02425441
  0.01940712  0.01741665  0.01542617  0.02164641
  0.01028811  0.00923292  0.00817773  0.01147520



Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
Shig4337             1.1395 (0.1912 0.1678)
CFT073               0.8470 (0.1897 0.2239) 0.0000 (0.0000 0.1451)
O157                 1.2846 (0.1897 0.1476) 0.0000 (0.0000 0.0387) 0.0000 (0.0000 0.1008)


TREE #  1:  ((1, 2), (3, 4));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):   -469.686430     +0.000000
   5..6     6..1     6..2     5..7     7..3     7..4  
  0.00000  0.74677  0.02752  0.00000  0.06980  0.00000  1.28094  0.73271  0.00000  0.00000  4.54018
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.84409

((1: 0.746770, 2: 0.027520): 0.000000, (3: 0.069797, 4: 0.000004): 0.000000);

((K12: 0.746770, Shig4337: 0.027520): 0.000000, (CFT073: 0.069797, O157: 0.000004): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  1.28094


dN/dS for site classes (K=3)

p:   0.73271  0.00000  0.26729
w:   0.00000  1.00000  4.54018

dN & dS for each branch

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

   5..6       0.000     62.8    165.2   1.2135   0.0000   0.0000    0.0    0.0
   6..1       0.747     62.8    165.2   1.2135   0.2616   0.2156   13.5   43.2
   6..2       0.028     62.8    165.2   1.2135   0.0096   0.0079    0.5    1.6
   5..7       0.000     62.8    165.2   1.2135   0.0000   0.0000    0.0    0.0
   7..3       0.070     62.8    165.2   1.2135   0.0245   0.0201    1.3    4.0
   7..4       0.000     62.8    165.2   1.2135   0.0000   0.0000    0.0    0.0


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

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

    51 M      1.000**       4.540
    52 V      1.000**       4.540
    53 G      1.000**       4.540
    61 Q      1.000**       4.540
    62 T      1.000**       4.540
    63 A      1.000**       4.540
    64 N      1.000**       4.540
    65 G      1.000**       4.540
    66 G      1.000**       4.540
    67 W      1.000**       4.540
    68 S      1.000**       4.540
    69 I      1.000**       4.540
    70 T      1.000**       4.540
    72 I      1.000**       4.540
    74 S      1.000**       4.540
    76 P      1.000**       4.540


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

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

    51 M      0.745         5.096 +- 3.026
    53 G      0.746         5.124 +- 3.115
    62 T      0.942         6.383 +- 2.409
    63 A      0.835         5.679 +- 2.832
    65 G      0.813         5.533 +- 2.887
    66 G      0.958*        6.472 +- 2.321
    67 W      0.935         6.336 +- 2.462
    69 I      0.866         5.889 +- 2.733
    70 T      0.923         6.260 +- 2.506
    74 S      0.531         3.689 +- 3.214
    76 P      0.605         4.185 +- 3.225



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:   0.537  0.281  0.117  0.043  0.014  0.005  0.002  0.001  0.000  0.000
w2:   0.002  0.020  0.072  0.133  0.169  0.170  0.150  0.121  0.093  0.070

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 0.001 0.001 0.001
 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.003 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.012 0.008 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.017 0.034 0.015 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.022 0.048 0.068 0.017 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.023 0.063 0.095 0.089 0.014 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.007 0.024 0.065 0.119 0.122 0.078 0.008 0.001

sum of density on p0-p1 =   1.000000
