
seed used = 139999613

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1490.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 417
# site patterns = 127
    9    6    8    9   14    3   15    5    8    2    5    8    1    8    2
    1    1   19    7    3   12    1   25    1    4   11   12    9   11    2
    7    5    5    9    6    4    4    3    5    1   11    7    3    1    1
    6    4    1    1    1    1    5    2    1    1    1    4    1    5    1
    4    1    1    1    4    1    1    2    1    1    1    1    2    1    1
    1    2    1    2    1    1    1    1    1    1    1    1    1    1    3
    2    1    2    1    2    1    1    1    5    1    1    2    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 GAG TAT TTT AAA AGA GAT TGG ACC GGA CTT GTC GAA CAG GCA CCG CCC ATT CGT GCT GCC GCG GAA GTT GCG CAT CTG AGT ATC CGA CGC GAC CCG TTC TTG AAT CAA GTT CGG AAG AAC GTG TCT AGG CTA ATA GTA GGG AAA CTC GTG TCG TCC TAC GCG ACT TCA AAG TTA ATC GGC AGT CCT AGC GGT TTT AGT GGT GCC GTA AGA AAT CTG TTA CAA CAC ACG CTA ACT ACA TCT CAG GCC TTT TAT GAC AAC GTC CGC AGT GAT TAT GTT TTC CGC TAC GGG GGC GAA TTT ATC ATT TTG ACT GCT TCT AAC ACG TTA CGT ACC GCA CGG GAG AAA ACC AAA AAA GCC GCA AAC GGC GAA GAT ATT CTC TCA 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T .T. ... ... ... ... ..A ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... G.. ... ..C ... ... ... ... ..C ..C ... ..G ..G .T. T.. C.. ..G ... ... ..G ... ... ..A --- --- ..C CTC TCG C.G AAG A.A --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- TT. A.A TCG .AA .T. GGC ..T .GG TCA TCG CGG A.G C.. G.. AGT 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ..G ... ..A ... ..T ... ..T ..C ... ..A ... ... ... ... ... ... ... ..C ..C ..C ..T ..G ..G ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 12 10 11 | Ser TCT  5  3  7 | Tyr TAT 10  8 10 | Cys TGT  0  0  0
    TTC 10 10 11 |     TCC  2  2  0 |     TAC  2  1  2 |     TGC  0  0  0
Leu TTA  7  5  7 |     TCA  5  6  5 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  7  9  7 |     TCG  5  8  5 |     TAG  0  0  0 | Trp TGG  5  5  5
--------------------------------------------------------------------------
Leu CTT  5  7  5 | Pro CCT  1  2  1 | His CAT 11 11 11 | Arg CGT  9  7  9
    CTC  2  3  2 |     CCC  1  0  1 |     CAC  1  1  1 |     CGC 10  7 10
    CTA  2  2  1 |     CCA  0  0  0 | Gln CAA  5  4  5 |     CGA  2  2  2
    CTG 14 13 15 |     CCG  6  5  6 |     CAG  9 10  9 |     CGG  6  6  6
--------------------------------------------------------------------------
Ile ATT 22 20 22 | Thr ACT  4  2  3 | Asn AAT  5  4  5 | Ser AGT 14 10 13
    ATC 13 11 13 |     ACC 10  9 11 |     AAC 14 11 14 |     AGC  1  3  2
    ATA  6  7  6 |     ACA  1  1  1 | Lys AAA 18 18 19 | Arg AGA  4  4  3
Met ATG  9  9  9 |     ACG  3  2  3 |     AAG  2  3  1 |     AGG  1  2  2
--------------------------------------------------------------------------
Val GTT  6  3  6 | Ala GCT  4  4  6 | Asp GAT 18 15 18 | Gly GGT  6  4  4
    GTC  9 10  9 |     GCC 15 13 14 |     GAC  6  5  6 |     GGC  6  7  8
    GTA  5  5  5 |     GCA  4  3  4 | Glu GAA 32 26 31 |     GGA  2  2  2
    GTG  8  8  8 |     GCG  6  5  5 |     GAG  7  6  8 |     GGG  2  2  2
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.16787    C:0.20144    A:0.30456    G:0.32614
position  2:    T:0.32854    C:0.17266    A:0.33573    G:0.16307
position  3:    T:0.31655    C:0.24460    A:0.22302    G:0.21583

#2: Shig4337       
position  1:    T:0.17585    C:0.20997    A:0.30446    G:0.30971
position  2:    T:0.34646    C:0.17060    A:0.32283    G:0.16010
position  3:    T:0.28871    C:0.24409    A:0.22310    G:0.24409

#3: O157           
position  1:    T:0.16787    C:0.20144    A:0.30456    G:0.32614
position  2:    T:0.32854    C:0.17266    A:0.33573    G:0.16307
position  3:    T:0.31415    C:0.24940    A:0.21823    G:0.21823

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      33 | Ser S TCT      15 | Tyr Y TAT      28 | Cys C TGT       0
      TTC      31 |       TCC       4 |       TAC       5 |       TGC       0
Leu L TTA      19 |       TCA      16 | *** * TAA       0 | *** * TGA       0
      TTG      23 |       TCG      18 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT      17 | Pro P CCT       4 | His H CAT      33 | Arg R CGT      25
      CTC       7 |       CCC       2 |       CAC       3 |       CGC      27
      CTA       5 |       CCA       0 | Gln Q CAA      14 |       CGA       6
      CTG      42 |       CCG      17 |       CAG      28 |       CGG      18
------------------------------------------------------------------------------
Ile I ATT      64 | Thr T ACT       9 | Asn N AAT      14 | Ser S AGT      37
      ATC      37 |       ACC      30 |       AAC      39 |       AGC       6
      ATA      19 |       ACA       3 | Lys K AAA      55 | Arg R AGA      11
Met M ATG      27 |       ACG       8 |       AAG       6 |       AGG       5
------------------------------------------------------------------------------
Val V GTT      15 | Ala A GCT      14 | Asp D GAT      51 | Gly G GGT      14
      GTC      28 |       GCC      42 |       GAC      17 |       GGC      21
      GTA      15 |       GCA      11 | Glu E GAA      89 |       GGA       6
      GTG      24 |       GCG      16 |       GAG      21 |       GGG       6
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.17037    C:0.20412    A:0.30453    G:0.32099
position  2:    T:0.33416    C:0.17202    A:0.33169    G:0.16214
position  3:    T:0.30700    C:0.24609    A:0.22140    G:0.22551

Codon frequencies under model, for use in evolver:
  0.01804342  0.01446376  0.01301255  0.01325442
  0.00928836  0.00744563  0.00669858  0.00682309
  0.01791009  0.01435688  0.00000000  0.00000000
  0.00875506  0.00701813  0.00000000  0.00643133
  0.02161724  0.01732856  0.01558991  0.01587969
  0.01112808  0.00892037  0.00802535  0.00817452
  0.02145750  0.01720052  0.01547471  0.01576235
  0.01048915  0.00840819  0.00756456  0.00770517
  0.03225152  0.02585310  0.02325914  0.02369147
  0.01660238  0.01330861  0.01197330  0.01219585
  0.03201321  0.02566206  0.02308728  0.02351641
  0.01564914  0.01254448  0.01128584  0.01149561
  0.03399485  0.02725056  0.02451639  0.02497209
  0.01749981  0.01402800  0.01262051  0.01285509
  0.03374365  0.02704920  0.02433524  0.02478756
  0.01649504  0.01322256  0.01189588  0.01211700



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             0.3516 (0.0435 0.1236)
O157                 0.0000 (0.0000 0.0623) 0.3648 (0.0435 0.1192)


TREE #  1:  ((1, 2), 3);   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -2040.971553     +0.000000
   4..5     5..1     5..2     4..3  
  0.01348  0.02465  0.31505  0.00842  2.50400  0.90030  0.04952  0.00000 21.99838
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.36161

((1: 0.024650, 2: 0.315054): 0.013480, 3: 0.008424);

((K12: 0.024650, Shig4337: 0.315054): 0.013480, O157: 0.008424);

Detailed output identifying parameters

kappa (ts/tv) =  2.50400


dN/dS for site classes (K=3)

p:   0.90030  0.04952  0.05018
w:   0.00000  1.00000 21.99838

dN & dS for each branch

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

   4..5       0.013    341.3    909.7   1.1534   0.0047   0.0040    1.4    4.2
   5..1       0.025    341.3    909.7   1.1534   0.0085   0.0074    2.5    7.8
   5..2       0.315    341.3    909.7   1.1534   0.1090   0.0945   32.2   99.1
   4..3       0.008    341.3    909.7   1.1534   0.0029   0.0025    0.9    2.7


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

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

    22 P      0.604         13.675
    32 V      0.587         13.332
   361 Y      0.977*        21.508
   362 D      0.999**       21.970
   363 N      0.949         20.928
   364 V      0.995**       21.885
   365 R      0.761         16.762
   400 R      0.969*        21.355
   402 E      0.718         16.073
   403 K      0.997**       21.936
   404 T      0.948         20.915
   405 K      0.519         11.897
   407 K      0.993**       21.851
   409 A      0.849         18.818
   410 N      0.999**       21.970
   411 G      0.999**       21.968
   412 E      0.987*        21.729
   413 D      0.861         19.076
   414 I      0.552         12.587
   416 L      0.688         15.454
   417 S      0.999**       21.979


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

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

    22 P      0.559         5.849 +- 4.766
    32 V      0.526         5.529 +- 4.793
   361 Y      0.958*        9.678 +- 1.953
   362 D      0.995**       10.009 +- 0.979
   363 N      0.945         9.559 +- 2.189
   364 V      0.990**       9.966 +- 1.154
   365 R      0.673         6.831 +- 4.680
   400 R      0.906         9.175 +- 2.840
   402 E      0.569         5.939 +- 4.767
   403 K      0.988*        9.948 +- 1.226
   404 T      0.913         9.250 +- 2.713
   407 K      0.990*        9.965 +- 1.157
   409 A      0.678         6.993 +- 4.493
   410 N      0.995**       10.009 +- 0.977
   411 G      0.992**       9.985 +- 1.084
   412 E      0.969*        9.775 +- 1.734
   413 D      0.893         9.083 +- 2.896
   414 I      0.502         5.301 +- 4.799
   416 L      0.599         6.229 +- 4.708
   417 S      0.995**       10.010 +- 0.974



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:   0.984  0.016  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.000  0.000  0.003  0.016  0.071  0.240  0.669

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 0.001
 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 0.000 0.000 0.007 0.029
 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 0.631 0.332

sum of density on p0-p1 =   1.000000
