
seed used = 140014333

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2928.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 237
# site patterns = 143
    4    5    2    8    2    3    6    3    8    1    1    1    1    5    3
    1    1    2    1    1    1    4    1    2    2    3    2    6    1    1
    1    6    1    1    1    4    5    1    1    2    2    1    5    1    2
    5    1    3    1    4    2    1    2    1    1    6    2    1    2    1
    1    2    2    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    2    1    1    1    1    1    1    2    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    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1

1       
K12                   GTG AAA ATT GAA TTA ACG AAT GGG CTG AAG ATA CAG GCA CAG TAC CAG AAC GAG ATT AAT GTA CAT CCG TTG CAC ATG TTG GCG GCC ACG GTA CCG CGG CGT ACG GTT TTT CTT TGC GCT GGT TCA ACC CTA TTC TGG GAA TAT CTC CAA GAC GAA CCC ACG CTC GAT CAC AGC GAT CGC GGC GCA CCA ACA ACG CGC CAG GTC TGT CGA AAG CCT TTG CTC GTC ATC GTC GGA AAC TTG TTA GAT GAA AAG CTG GAG TTG GCA TCT TTC TGC TTT TCT ATT CAT GCA CCT GCT CAA ATT CTG CGG GAG CGC ATT AGT CGT AAA ATT GGA GGA TTA ACG CGG CAA GTA GCC GCA GCC CGC GAT GGC CCC GTC GAG CGT GTG ATG AAT AGC CGT CAG ATA GTA GAG ACT GAA GAA GGC CGG TTC ACA AGC 
Shig4337              ... ... ... ... ... ... ... ... ... ..C G.G ..A ..G ... ... ..T G.T ... ..A CGC ..G ... .T. ... .GT ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ..G ... G.. ... ... ... ... ..C ... ... ... ... ... G.. ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ..G ..C ..G ... TGC C.. C.T ..G CAA ..T ..T ..C ..G ..C A.C ..G ..A ... GCT GCG T.. ... ... ..T G.G G.G ..C ..G C.G ... ..G G.. T.. .T. GC. .AT ..A ..C .A. ..T ..C ..G ..G ..T CGC ..G .G. GAA G.G ..T .TG .CT .CC T.. AT. ..C .CT ACG ..T GAA C.G GTG GAT 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .GT ... C.. ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... G.. T.. .G. ..T ... ... ... ... C.. ... ... ... ... ..T ... ... ..G ... ... ... TGC C.. C.T ..G CAA ..T ..T ..C ..G ..C A.A ..T ..C ..A TCT GCG T.. ... ... ..T G.G G.G ..C ..G C.G ... ..G ... T.. .T. GC. .AC ..A ..C .A. ..T ..C ..G ..G ..T CGC ..G ... GAA G.G ..T .TG .CT .CC T.. AT. ..C .CT ACG ..T GAA C.G .TG GAT 
O157                  ... ... ... ... ... ... ... ... ... ..C G.G ..A ..G ... ... ..T G.T ... ..A CGC ..G ... ... ... .GT ... C.. ... ... ... ... ... ..C ..A ..C ... ... ... ... ... ... ..T ... ... ... ... .C. ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... A.A A.. ... ... ... ... C.A ..G ..C ..T ..C .GC C.. C.A ..G CAA ..T ..T ..C ..G ..C A.. ..G ..A ... ACT GCG T.. ... ..A ..A G.G G.G ..C ..G C.G ... ..G ... T.. .T. GC. .AC ..A ..T .A. ..T ..C ..G ..G ..T CGC ..G ... GAA G.G ..T .TG .CT .CC T.. AT. ..C .CT ACG ..T GAA C.G GTG GAT 

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

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

#1: K12            
position  1:    T:0.16034    C:0.28270    A:0.22785    G:0.32911
position  2:    T:0.29114    C:0.21941    A:0.33755    G:0.15190
position  3:    T:0.25738    C:0.19831    A:0.21519    G:0.32911

#2: Shig4337       
position  1:    T:0.15612    C:0.29114    A:0.18143    G:0.37131
position  2:    T:0.28692    C:0.23207    A:0.32068    G:0.16034
position  3:    T:0.24051    C:0.19409    A:0.17300    G:0.39241

#3: CFT073         
position  1:    T:0.16456    C:0.28692    A:0.20253    G:0.34599
position  2:    T:0.28692    C:0.23629    A:0.32068    G:0.15612
position  3:    T:0.25738    C:0.17722    A:0.18987    G:0.37553

#4: O157           
position  1:    T:0.15190    C:0.29536    A:0.19831    G:0.35443
position  2:    T:0.28692    C:0.24051    A:0.31646    G:0.15612
position  3:    T:0.24473    C:0.19409    A:0.19831    G:0.36287

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      24 | Ser S TCT       6 | Tyr Y TAT      12 | Cys C TGT       7
      TTC      13 |       TCC       0 |       TAC      12 |       TGC       8
Leu L TTA      15 |       TCA       1 | *** * TAA       0 | *** * TGA       0
      TTG      26 |       TCG       6 |       TAG       0 | Trp W TGG      20
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       8 | His H CAT      19 | Arg R CGT      17
      CTC      10 |       CCC      10 |       CAC      10 |       CGC      19
      CTA       6 |       CCA      10 | Gln Q CAA      23 |       CGA       6
      CTG      56 |       CCG      30 |       CAG      31 |       CGG      13
------------------------------------------------------------------------------
Ile I ATT      15 | Thr T ACT       2 | Asn N AAT      28 | Ser S AGT       4
      ATC      11 |       ACC      27 |       AAC      10 |       AGC       6
      ATA       6 |       ACA       6 | Lys K AAA      22 | Arg R AGA       0
Met M ATG      17 |       ACG      26 |       AAG      12 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      20 | Ala A GCT      17 | Asp D GAT      40 | Gly G GGT      12
      GTC      10 |       GCC       9 |       GAC      20 |       GGC       6
      GTA       9 |       GCA      24 | Glu E GAA      48 |       GGA       8
      GTG      29 |       GCG      38 |       GAG      20 |       GGG      22
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15823    C:0.28903    A:0.20253    G:0.35021
position  2:    T:0.28797    C:0.23207    A:0.32384    G:0.15612
position  3:    T:0.25000    C:0.19093    A:0.19409    G:0.36498

Codon frequencies under model, for use in evolver:
  0.01178553  0.00900076  0.00914995  0.01720588
  0.00949750  0.00725336  0.00737358  0.01386554
  0.01325333  0.01012174  0.00000000  0.00000000
  0.00638923  0.00487954  0.00000000  0.00932773
  0.02152824  0.01644140  0.01671390  0.03142941
  0.01734876  0.01324948  0.01346908  0.02532773
  0.02420941  0.01848904  0.01879549  0.03534369
  0.01167099  0.00891328  0.00906102  0.01703865
  0.01508548  0.01152098  0.01171193  0.02202353
  0.01215680  0.00928430  0.00943819  0.01774790
  0.01696426  0.01295583  0.01317056  0.02476638
  0.00817821  0.00624580  0.00634933  0.01193949
  0.02608531  0.01992169  0.02025188  0.03808235
  0.02102113  0.01605411  0.01632020  0.03068907
  0.02933403  0.02240278  0.02277410  0.04282521
  0.01414149  0.01080004  0.01097904  0.02064538



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                 
Shig4337             0.2556 (0.1227 0.4800)
CFT073               0.2623 (0.1049 0.4000) 0.2312 (0.0295 0.1275)
O157                 0.2346 (0.1203 0.5129) 0.2305 (0.0209 0.0904) 0.1982 (0.0334 0.1686)


TREE #  1:  ((1, 2), (3, 4));   MP score: 123
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):  -1616.008954     +0.000000
   5..6     6..1     6..2     5..7     7..3     7..4  
  0.00000  0.74954  0.04752  0.00000  0.13625  0.08507  2.12671  0.71078  0.27417  0.00000 10.18374
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.01838

((1: 0.749538, 2: 0.047516): 0.000000, (3: 0.136254, 4: 0.085072): 0.000000);

((K12: 0.749538, Shig4337: 0.047516): 0.000000, (CFT073: 0.136254, O157: 0.085072): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.12671


dN/dS for site classes (K=3)

p:   0.71078  0.27417  0.01505
w:   0.00000  1.00000 10.18374

dN & dS for each branch

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

   5..6       0.000    196.1    514.9   0.4274   0.0000   0.0000    0.0    0.0
   6..1       0.750    196.1    514.9   0.4274   0.1825   0.4268   83.7   94.0
   6..2       0.048    196.1    514.9   0.4274   0.0116   0.0271    5.3    6.0
   5..7       0.000    196.1    514.9   0.4274   0.0000   0.0000    0.0    0.0
   7..3       0.136    196.1    514.9   0.4274   0.0332   0.0776   15.2   17.1
   7..4       0.085    196.1    514.9   0.4274   0.0207   0.0484    9.5   10.7


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

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

    23 N      0.924         9.482
   162 L      0.723         7.636
   179 Q      0.941         9.643


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

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

    23 N      0.928         5.305 +- 2.700
   162 L      0.853         4.936 +- 2.840
   179 Q      0.953*        5.392 +- 2.636



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:   0.993  0.007  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.055  0.129  0.139  0.142  0.129  0.112  0.095  0.079  0.065  0.054

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 0.007
 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 0.008 0.490
 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 0.019 0.201 0.174
 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 0.044 0.019 0.001

sum of density on p0-p1 =   1.000000
