
seed used = 140019909

K12                                  GTG GTG CGT AAC GGC AAA AGC ACC GCC GGA CAT CAG CGC TAT CTC TGC TCT CAC TGC CGT AAA ACA TGG CAA CTG CAG TTC ACT TAC ACC GCT TCT CAA CCC GGT ACG CAC CAG AAA ATC ATT GAT ATG GCC ATG AAT GGC GTT GGA TGC CGG GCA ACA GCC CGC ATT ATG GGC GTT GGC CTC AAC ACG ATT TTA CGT CAC TTA AAA AAC TCA GGC CGC AGT CGG 
S2457T                               GTG GTG CGT AAC GGC AAA AGC ACT GCC GGA CAT CAG CGC TAT CTC TGC TCT CAT TGC CGT AAA ACA TGG CAA CTA CAG TTC ACT TAC ACC GCC TCT CAG CCC GGT ACG CAC CAG AAA ATC ATT GAT ATG GCC ATG AAT GGC GTC GGA TGT CGC GCC AGT GCA CGC ATT ATG GGC GTT GGC CTC AAC ACG GTT TTA CGT CAC TTA AAA AAC TCA GGC CGC AGT CGG 
Shig4337                             GTG GTG CGT AAC GGC AAA AGC ACC GCC GGA CAT CAG CGC TAT CTC TGC TCT CAC TGC CGT AAA ACA TGG CAA CTG CAG TTC ACT TAC ACC GCT TCT CAA CCC GGT ACG CAC CAG AAA ATC ATT GAT ATG GCC ATG AAT GGC GTT GGA TGC CGG GCA ACC GCC CGC ATT ATG GGC GTT GGC CTC AAC ACG ATT TTC CGC CAT TTA AAA AAC TCA GGC CGC AGT CGG 
O157                                 GTG GTG CGT AAC GGC AAA AGC ACT GCC GGA CAT CAG CGC TAT CTC TGC TCT CCT TGC CGT AAA ACA TGG CAA CTA CAG TTC ACT TAC ACC GCC TCT CAG CCC GGT AAG CAC CAG AAA ATC ATT GAT ATG GCC ATG AAT GGC GTC GGA TGT CGC GCC AGT GCA CGC ATT ATG GGC GTT GGC CTC AAC ACG GTT TTA CGT CAC TTA AAA AAC TCA GGC CGC AGT CGG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3444.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 75
# site patterns = 52
    2    2    3    5    4    1    1    2    2    1    3    3    1    2    2
    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    2    1    3    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1

1       
K12                   GTG CGT AAC GGC AAA AGC ACC GCC GGA CAT CAG CGC TAT CTC TGC TCT CAC ACA TGG CAA CTG TTC ACT TAC ACC GCT CAA CCC GGT ACG CAC ATC ATT GAT ATG AAT GTT TGC CGG GCA ACA GCC GTT ACG ATT TTA CGT CAC TTA TCA AGT CGG 
S2457T                ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ..T ... ... ... ..A ... ... ... ... ..C ..G ... ... ... ... ... ... ... ... ... ..C ..T ..C ..C .GT ..A ... ... G.. ... ... ... ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..C ..C ..T ... ... ... ... 
O157                  ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... .CT ... ... ... ..A ... ... ... ... ..C ..G ... ... .A. ... ... ... ... ... ... ..C ..T ..C ..C .GT ..A ... ... G.. ... ... ... ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.16000    C:0.28000    A:0.32000    G:0.24000
position  2:    T:0.22667    C:0.21333    A:0.26667    G:0.29333
position  3:    T:0.24000    C:0.38667    A:0.18667    G:0.18667

#2: S2457T         
position  1:    T:0.16000    C:0.28000    A:0.30667    G:0.25333
position  2:    T:0.22667    C:0.20000    A:0.26667    G:0.30667
position  3:    T:0.26667    C:0.38667    A:0.17333    G:0.17333

#3: Shig4337       
position  1:    T:0.16000    C:0.28000    A:0.32000    G:0.24000
position  2:    T:0.22667    C:0.21333    A:0.26667    G:0.29333
position  3:    T:0.24000    C:0.41333    A:0.16000    G:0.18667

#4: O157           
position  1:    T:0.16000    C:0.28000    A:0.30667    G:0.25333
position  2:    T:0.22667    C:0.20000    A:0.26667    G:0.30667
position  3:    T:0.26667    C:0.38667    A:0.17333    G:0.17333

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       0 | Ser S TCT       8 | Tyr Y TAT       4 | Cys C TGT       2
      TTC       5 |       TCC       0 |       TAC       4 |       TGC      10
Leu L TTA       7 |       TCA       4 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       0 |       TAG       0 | Trp W TGG       4
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       1 | His H CAT       6 | Arg R CGT      11
      CTC       8 |       CCC       4 |       CAC       9 |       CGC      15
      CTA       2 |       CCA       0 | Gln Q CAA       6 |       CGA       0
      CTG       2 |       CCG       0 |       CAG      14 |       CGG       6
------------------------------------------------------------------------------
Ile I ATT      10 | Thr T ACT       6 | Asn N AAT       4 | Ser S AGT       6
      ATC       4 |       ACC       7 |       AAC      12 |       AGC       4
      ATA       0 |       ACA       5 | Lys K AAA      16 | Arg R AGA       0
Met M ATG      12 |       ACG       7 |       AAG       1 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       8 | Ala A GCT       2 | Asp D GAT       4 | Gly G GGT       4
      GTC       2 |       GCC      14 |       GAC       0 |       GGC      20
      GTA       0 |       GCA       4 | Glu E GAA       0 |       GGA       8
      GTG       8 |       GCG       0 |       GAG       0 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16000    C:0.28000    A:0.31333    G:0.24667
position  2:    T:0.22667    C:0.20667    A:0.26667    G:0.30000
position  3:    T:0.25333    C:0.39333    A:0.17333    G:0.18000

Codon frequencies under model, for use in evolver:
  0.00940765  0.01460662  0.00643682  0.00668438
  0.00857757  0.01331780  0.00586886  0.00609459
  0.01106783  0.01718426  0.00000000  0.00000000
  0.01245131  0.01933229  0.00000000  0.00884698
  0.01646339  0.02556158  0.01126443  0.01169767
  0.01501074  0.02330615  0.01027051  0.01066553
  0.01936870  0.03007245  0.01325227  0.01376197
  0.02178978  0.03383151  0.01490880  0.01548222
  0.01842332  0.02860463  0.01260543  0.01309025
  0.01679773  0.02608069  0.01149319  0.01193523
  0.02167449  0.03365250  0.01482992  0.01540030
  0.02438381  0.03785907  0.01668366  0.01732534
  0.01450346  0.02251854  0.00992342  0.01030509
  0.01322375  0.02053161  0.00904783  0.00939582
  0.01706290  0.02649240  0.01167462  0.01212364
  0.01919576  0.02980395  0.01313394  0.01363909



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               0.0664 (0.0148 0.2230)
Shig4337             0.1030 (0.0059 0.0571) 0.0614 (0.0178 0.2892)
O157                 0.1206 (0.0269 0.2228)-1.0000 (0.0118 0.0000) 0.1034 (0.0299 0.2889)


TREE #  1:  ((1, (2, 3)), 4);   MP score: 28
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):   -427.693039     +0.000000
   5..6     6..1     6..7     7..2     7..3     5..4  
  0.03007  0.22077  0.00000  0.00000  0.27089  0.00000  1.98185  0.91446  0.00000  0.00000  1.56888
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.52173

((1: 0.220774, (2: 0.000004, 3: 0.270885): 0.000000): 0.030065, 4: 0.000004);

((K12: 0.220774, (S2457T: 0.000004, Shig4337: 0.270885): 0.000000): 0.030065, O157: 0.000004);

Detailed output identifying parameters

kappa (ts/tv) =  1.98185


dN/dS for site classes (K=3)

p:   0.91446  0.00000  0.08554
w:   0.00000  1.00000  1.56888

dN & dS for each branch

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

   5..6       0.030     55.8    169.2   0.1342   0.0039   0.0287    1.6    0.7
   6..1       0.221     55.8    169.2   0.1342   0.0283   0.2110   11.8    4.8
   6..7       0.000     55.8    169.2   0.1342   0.0000   0.0000    0.0    0.0
   7..2       0.000     55.8    169.2   0.1342   0.0000   0.0000    0.0    0.0
   7..3       0.271     55.8    169.2   0.1342   0.0347   0.2588   14.4    5.9
   5..4       0.000     55.8    169.2   0.1342   0.0000   0.0000    0.0    0.0


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

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

    18 H      1.000**       1.569
    36 T      1.000**       1.569
    53 T      1.000**       1.569
    64 I      1.000**       1.569
    65 L      1.000**       1.569


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

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

    53 T      0.772         4.203 +- 2.955



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:   0.145  0.154  0.141  0.120  0.101  0.086  0.074  0.066  0.059  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 0.000
 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 0.003
 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 0.005 0.090
 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 0.017 0.128 0.755

sum of density on p0-p1 =   1.000000
