
seed used = 140020601

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3490.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 443
# site patterns = 184
    5   20    1    1    1   20    1    1    1    1    9    1    6    1   15
    1   19    6   11    1    1    5    3    1    1    3    1    1    9    8
    1    1    3    2    1    2    6   13    5    1   13    3    1    1    5
    1    3    1    1    1    5    1    1    1    5    1    1    1    1    7
    8    1    1    2    2    1    5    1    4    3    2    4    2    1    9
    1    1    1    1    1    1    7    1    1    1    1    2    3    1    1
    1    1    5    1    1    1    2    1    1    1    1    1    1    1    1
    4    4    3    4    1    4    4    1    1    1    1    1    1    2    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    2    1
    1    2    2    1    1    1    1    1    1    1    1    1    1    1    1
    2    1    2    1    1    1    1    1    2    1    1    1    2    1    1
    1    3    1    1    1    1    1    1    1    1    1    3    2    1    1
    1    1    1    1

K12                                  ATG AAA GCA ATT GAC AAT CAG ATT AGA AAC ATC TCT TCA AGC CAT CAA GAT AAG GTT AAC AGT CAA CAC GGC ACA CGT GCA AAG ATA GAA TTT AAA CTG AAT GAT TCG AAC TTT GGC CTG TAT TTC GGT CAC TGG AAG GTA AAT GAT CGT AGT CAC CAG ATG GAG GTA TAT GAA CCT TCT ATT CAA AGA TTC GCC GAC ACT GAT ACG ACA CCA GAC GTG TTA TTA CCC ACC ACT GTT TGT GGC GGT TCC TCT GGA GAT GAT GGG CTT ATA GCG AGA CTT AGT CCT GAT GTC ACT GAA AGC AAA GTG TCA TTC CAG TGT GCT GGA AGA GCA TTG CTC AGG GGT GAA TTA GAG TCT GCA TAC AAA CAT AAT GTG TAC GAT AAT ACG ATC AAG GAC GCG ATA ACC CCT TTT CTA CGA AGC ATT GTC ACT GCA CAT GCC ACG GAC AGG CAA AGA --- --- --- --- --- --- --- --- --- --- --- --- --- AAT GTT ATT --- --- --- --- GTC TCG GTG CTT TGC AGG --- --- --- --- --- TTC TTA ATC 
Shig4337                             ... ... ... ... ... ... ATA T.. .AG T.. ... C.. ... .A. ... A.. ... ... ... ..T .A. ... ... A.. ... ... T.. ... ... ... A.. ..G ... ... ... ... ... ... ... A.. ... ... ... ... ... .G. ... ... ..A .A. ... .TT ... ... ... A.. ..C ..G ..A ... ... ... ..T ..T ... ..T ... A.C ... ... ... ... ... A.. ... ... ..A .AG A.. ... .AT ... .T. ..C ... ..C A.. ... ... ... C.T GA. ... ..C G.. ... ... C.. ..T ... ... ... ..T ..T ..A ... ... ... ... T.. ... ... ... ... ... ... ..C ... ... ... .T. ... ... T.. ... A.. ... ... ..A ... ... ... ... ... ... ... ... ... ... ... A.. ... .A. T.. ... ... A.. .CT A.. ... AAT CAA TGT TAT CTC GGT GCT TTG CAG GTT CCA TTT ATG G.C CCA ... GAT CCT GAG GAA T.A G.A AAT A.A ..T .AT AAA CAT CAA CAC CTT C.. C.. ..T 
O157                                 ... ... .T. T.. C.. ... ATA T.. .AG T.. ... ... ... .A. ... ... ... ... ... ..T .A. ... ... ... .A. ... T.. G.. ... ... A.. ..G ... ..A C.. ... ... ... ... ... ... ... ..C TG. ... ..C ... .C. ..A .A. ... .CT ... ..A ... A.. ..C ..G ..A ... ... A.. ..T ... ... ... ... ..C ... ... ... ... ... A.. ... ... ... ..G A.. C.. .A. ... .T. ..C ..G ..C ... ... T.. .A. .A. ... ... ... ... .C. ... ... ... ... G.. ..T ... ..T ... ... ... ... ... ... ... ... ... ..G ..T ..G ..C .TC ... ..T G.. A.. TTG AAA .T. AC. G.. .A. ... ..A .G. ... ..T ... ... ..C ... ... ..T ..A ..T .G. ... ... T.. ..A ... ... ..T ..G AAT AAA TGT TAT CTC GGT GCT TTG CAG GTT CCA TTT ATG ... CC. .C. GAT CCT GAG GAA T.A G.A TAT A.A .TT .AT AAA CAT CAA CAT CTT ... C.. ..T 



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 15 19 19 | Ser TCT 10  9  8 | Tyr TAT 14 15 16 | Cys TGT  5  8  6
    TTC  7  4 10 |     TCC  1  1  2 |     TAC  2  4  2 |     TGC  1  0  1
Leu TTA 12 11 10 |     TCA  7  8  8 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  4  6  7 |     TCG  3  2  2 |     TAG  0  0  0 | Trp TGG  5  5  5
--------------------------------------------------------------------------
Leu CTT  7  8  6 | Pro CCT  3  5  5 | His CAT 17 19 22 | Arg CGT  4  3  4
    CTC  4  6  5 |     CCC  1  1  1 |     CAC  5  5  4 |     CGC  0  0  0
    CTA  2  3  3 |     CCA  2  5  4 | Gln CAA  8  9  7 |     CGA  2  2  2
    CTG  4  3  4 |     CCG  0  0  0 |     CAG  3  3  4 |     CGG  0  0  0
--------------------------------------------------------------------------
Ile ATT 12 14 12 | Thr ACT  8  7  9 | Asn AAT 26 34 27 | Ser AGT  7  6  9
    ATC 11 10 10 |     ACC  3  2  3 |     AAC  8  9  8 |     AGC  3  4  1
    ATA 11 17 15 |     ACA  4  5  4 | Lys AAA 23 26 31 | Arg AGA  8  5  5
Met ATG  6  9  7 |     ACG  6  6  5 |     AAG  9 11  9 |     AGG  3  2  3
--------------------------------------------------------------------------
Val GTT 13 12 14 | Ala GCT  4  6  6 | Asp GAT 27 27 26 | Gly GGT  9 10  8
    GTC  4  2  2 |     GCC  3  3  2 |     GAC  8  9 10 |     GGC  7  5  8
    GTA  4  3  4 |     GCA  6  4  5 | Glu GAA 11 13 13 |     GGA  4  4  3
    GTG  5  3  2 |     GCG  2  1  1 |     GAG  6  7  9 |     GGG  3  3  5
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.20874    C:0.15049    A:0.35922    G:0.28155
position  2:    T:0.29369    C:0.15291    A:0.40534    G:0.14806
position  3:    T:0.43932    C:0.16505    A:0.25243    G:0.14320

#2: Shig4337       
position  1:    T:0.20767    C:0.16253    A:0.37698    G:0.25282
position  2:    T:0.29345    C:0.14673    A:0.43115    G:0.12867
position  3:    T:0.45598    C:0.14673    A:0.25959    G:0.13770

#3: O157           
position  1:    T:0.21670    C:0.16027    A:0.35666    G:0.26637
position  2:    T:0.29345    C:0.14673    A:0.42438    G:0.13544
position  3:    T:0.44470    C:0.15576    A:0.25734    G:0.14221

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      53 | Ser S TCT      27 | Tyr Y TAT      45 | Cys C TGT      19
      TTC      21 |       TCC       4 |       TAC       8 |       TGC       2
Leu L TTA      33 |       TCA      23 | *** * TAA       0 | *** * TGA       0
      TTG      17 |       TCG       7 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT      21 | Pro P CCT      13 | His H CAT      58 | Arg R CGT      11
      CTC      15 |       CCC       3 |       CAC      14 |       CGC       0
      CTA       8 |       CCA      11 | Gln Q CAA      24 |       CGA       6
      CTG      11 |       CCG       0 |       CAG      10 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      38 | Thr T ACT      24 | Asn N AAT      87 | Ser S AGT      22
      ATC      31 |       ACC       8 |       AAC      25 |       AGC       8
      ATA      43 |       ACA      13 | Lys K AAA      80 | Arg R AGA      18
Met M ATG      22 |       ACG      17 |       AAG      29 |       AGG       8
------------------------------------------------------------------------------
Val V GTT      39 | Ala A GCT      16 | Asp D GAT      80 | Gly G GGT      27
      GTC       8 |       GCC       8 |       GAC      27 |       GGC      20
      GTA      11 |       GCA      15 | Glu E GAA      37 |       GGA      11
      GTG      10 |       GCG       4 |       GAG      22 |       GGG      11
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.21109    C:0.15794    A:0.36441    G:0.26656
position  2:    T:0.29353    C:0.14869    A:0.42065    G:0.13713
position  3:    T:0.44684    C:0.15562    A:0.25655    G:0.14099

Codon frequencies under model, for use in evolver:
  0.02892299  0.01007318  0.01660579  0.00912570
  0.01465128  0.00510269  0.00841186  0.00462273
  0.04144870  0.01443558  0.00000000  0.00000000
  0.01351258  0.00470611  0.00000000  0.00426345
  0.02163947  0.00753650  0.01242404  0.00682762
  0.01096172  0.00381770  0.00629354  0.00345861
  0.03101089  0.01080034  0.01780453  0.00978447
  0.01010978  0.00352099  0.00580441  0.00318981
  0.04992911  0.01738910  0.02866620  0.01575350
  0.02529217  0.00880865  0.01452120  0.00798012
  0.07155195  0.02491982  0.04108069  0.02257588
  0.02332646  0.00812404  0.01339261  0.00735990
  0.03652320  0.01272015  0.02096935  0.01152370
  0.01850125  0.00644354  0.01062227  0.00583746
  0.05234033  0.01822887  0.03005057  0.01651428
  0.01706333  0.00594275  0.00979671  0.00538378



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             0.4689 (0.0610 0.1302)
O157                 0.5021 (0.0745 0.1484) 0.5851 (0.0674 0.1151)


TREE #  1:  ((1, 2), 3);   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  4  np:  9):  -2453.782633     +0.000000
   4..5     5..1     5..2     4..3  
  0.23221  0.32017  0.26439  0.14484  2.13390  0.55271  0.43190  0.04890 87.16428
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.96161

((1: 0.320165, 2: 0.264389): 0.232208, 3: 0.144844);

((K12: 0.320165, Shig4337: 0.264389): 0.232208, O157: 0.144844);

Detailed output identifying parameters

kappa (ts/tv) =  2.13390


dN/dS for site classes (K=3)

p:   0.55271  0.43190  0.01539
w:   0.04890  1.00000 87.16428

dN & dS for each branch

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

   4..5       0.232    262.8   1066.2   1.8006   0.0849   0.0471   12.4   90.5
   5..1       0.320    262.8   1066.2   1.8006   0.1170   0.0650   17.1  124.8
   5..2       0.264    262.8   1066.2   1.8006   0.0966   0.0537   14.1  103.0
   4..3       0.145    262.8   1066.2   1.8006   0.0529   0.0294    7.7   56.4


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

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

     7 Q      0.805         70.393
   157 A      0.922         80.421
   265 N      0.913         79.648
   267 V      0.969*        84.468
   416 V      0.757         66.256
   424 V      0.970*        84.593


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

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

     7 Q      0.831         6.819 +- 3.263
    68 H      0.715         5.933 +- 3.653
    70 K      0.570         4.813 +- 3.802
    76 H      0.508         4.350 +- 3.786
   157 A      0.846         6.949 +- 3.195
   265 N      0.921         7.470 +- 2.729
   267 V      0.978*        7.861 +- 2.258
   383 R      0.569         4.796 +- 3.844
   384 Q      0.536         4.546 +- 3.786
   416 V      0.625         5.247 +- 3.795
   424 V      0.957*        7.723 +- 2.442



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:   0.180  0.284  0.345  0.176  0.016  0.000  0.000  0.000  0.000  0.000
w2:   0.002  0.013  0.027  0.050  0.087  0.121  0.149  0.171  0.186  0.194

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 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.081
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.027 0.172
 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 0.064 0.170
 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 0.002 0.007 0.090 0.143
 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 0.004 0.010 0.110 0.106

sum of density on p0-p1 =   1.000000
