
seed used = 140004605

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1993.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 179
# site patterns = 72
    1    1    8    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    6    4    4    3    3    5    2
    3    4    2    8    6    4    5    3    1    7    5    1    3    3    1
    4    2    2    8    2    2    5    1    4    1    3    2    2    2    3
    1    3    3    3    1    1    4    2    2    1    1    1

K12                                  ATT TTG GTG ACG GGG GGC GCA CGG AGC GGG AAG AGT CGC CAC GCA GAG GCG CTT ATT GGG GAC TCT TCA CAG GTT CTG TAT ATC GCT ACC TCG CAA CTT GAT GAG ATG GCA CGG ATA GAA CAT GGC CGC CCG CAC TGG ACA TTA ATT GAC AAC AAT GTT TTG CTT TGC ACT TTT GGC AAA CCT GCG GCC CGT CCC AAG GTA GGA GGG AGT CGA GGT 
Shig4337                             ..G G.A ... T.C --- --- --- --- --- --- --- --- --- --- ..T ATT ..C AG. .CA CCT C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... .C. ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                               ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... .C. ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 



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

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

#1: K12            
position  1:    T:0.13408    C:0.23464    A:0.22346    G:0.40782
position  2:    T:0.29050    C:0.20112    A:0.31844    G:0.18994
position  3:    T:0.31844    C:0.15642    A:0.18994    G:0.33520

#2: Shig4337       
position  1:    T:0.14201    C:0.23669    A:0.23077    G:0.39053
position  2:    T:0.29586    C:0.22485    A:0.31953    G:0.15976
position  3:    T:0.33136    C:0.15385    A:0.20118    G:0.31361

#3: CFT073         
position  1:    T:0.13408    C:0.23464    A:0.22905    G:0.40223
position  2:    T:0.29050    C:0.20112    A:0.31844    G:0.18994
position  3:    T:0.31285    C:0.15642    A:0.19553    G:0.33520

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       6 | Ser S TCT       3 | Tyr Y TAT       9 | Cys C TGT       0
      TTC       0 |       TCC       1 |       TAC       0 |       TGC       9
Leu L TTA       6 |       TCA       3 | *** * TAA       0 | *** * TGA       0
      TTG      14 |       TCG       9 |       TAG       0 | Trp W TGG      12
------------------------------------------------------------------------------
Leu L CTT       9 | Pro P CCT       4 | His H CAT      15 | Arg R CGT       9
      CTC       0 |       CCC       3 |       CAC       6 |       CGC      11
      CTA       0 |       CCA       0 | Gln Q CAA      12 |       CGA       3
      CTG      14 |       CCG       9 |       CAG      18 |       CGG      11
------------------------------------------------------------------------------
Ile I ATT      29 | Thr T ACT       6 | Asn N AAT      15 | Ser S AGT       6
      ATC       9 |       ACC       6 |       AAC       6 |       AGC       4
      ATA       3 |       ACA       7 | Lys K AAA       9 | Arg R AGA       0
Met M ATG      13 |       ACG       2 |       AAG       5 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      13 | Ala A GCT      18 | Asp D GAT      24 | Gly G GGT       3
      GTC       0 |       GCC      10 |       GAC       8 |       GGC       9
      GTA      13 |       GCA      19 | Glu E GAA      21 |       GGA       7
      GTG      25 |       GCG      10 |       GAG      20 |       GGG      11
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13662    C:0.23529    A:0.22770    G:0.40038
position  2:    T:0.29222    C:0.20873    A:0.31879    G:0.18027
position  3:    T:0.32068    C:0.15560    A:0.19545    G:0.32827

Codon frequencies under model, for use in evolver:
  0.01316660  0.00638853  0.00802461  0.01347823
  0.00940471  0.00456323  0.00573187  0.00962731
  0.01436356  0.00696930  0.00000000  0.00000000
  0.00812225  0.00394097  0.00000000  0.00831449
  0.02267580  0.01100246  0.01382016  0.02321251
  0.01619700  0.00785890  0.00987155  0.01658036
  0.02473724  0.01200268  0.01507654  0.02532274
  0.01398832  0.00678723  0.00852543  0.01431940
  0.02194433  0.01064754  0.01337435  0.02246372
  0.01567452  0.00760539  0.00955311  0.01604551
  0.02393926  0.01161550  0.01459020  0.02450587
  0.01353708  0.00656829  0.00825041  0.01385749
  0.03858544  0.01872193  0.02351657  0.03949870
  0.02756103  0.01337281  0.01679755  0.02821336
  0.04209321  0.02042392  0.02565444  0.04308949
  0.02380271  0.01154924  0.01450697  0.02436608



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             0.5918 (0.0367 0.0620)
CFT073               0.4696 (0.0074 0.0157) 0.6395 (0.0339 0.0531)


TREE #  1:  ((1, 2), 3);   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -834.089542     +0.000000
   4..5     5..1     5..2     4..3  
  0.00000  0.02975  0.44662  0.00000  1.33288  0.95198  0.00000  0.28161 138.65467
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.47637

((1: 0.029750, 2: 0.446619): 0.000000, 3: 0.000004);

((K12: 0.029750, Shig4337: 0.446619): 0.000000, CFT073: 0.000004);

Detailed output identifying parameters

kappa (ts/tv) =  1.33288


dN/dS for site classes (K=3)

p:   0.95198  0.00000  0.04802
w:   0.28161  1.00000138.65467

dN & dS for each branch

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

   4..5       0.000    132.5    404.5   6.9257   0.0000   0.0000    0.0    0.0
   5..1       0.030    132.5    404.5   6.9257   0.0126   0.0018    0.2    5.1
   5..2       0.447    132.5    404.5   6.9257   0.1887   0.0272    3.6   76.3
   4..3       0.000    132.5    404.5   6.9257   0.0000   0.0000    0.0    0.0


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

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

     2 L      0.906         125.701
     4 T      0.964*        133.661
    16 E      1.000**       138.627
    17 A      1.000**       138.627
    18 L      0.994**       137.882
    19 I      0.934         129.521
    20 G      1.000**       138.632


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

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

     1 I      0.583         5.584 +- 4.264
     2 L      0.665         6.299 +- 4.133
     4 T      0.672         6.354 +- 4.114
    16 E      0.987*        8.976 +- 1.834
    17 A      0.944         8.634 +- 2.436
    18 L      0.942         8.612 +- 2.464
    19 I      0.684         6.467 +- 4.085
    20 G      0.958*        8.750 +- 2.262
    21 D      0.631         5.999 +- 4.201
    48 G      0.657         6.226 +- 4.148
    75 V      0.602         5.752 +- 4.244



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:   0.257  0.197  0.150  0.113  0.085  0.064  0.048  0.037  0.028  0.022
w2:   0.001  0.003  0.007  0.016  0.032  0.058  0.099  0.161  0.249  0.375

Posterior for p0-p1 (see the ternary graph)

 0.003
 0.007 0.009 0.003
 0.001 0.005 0.010 0.012 0.004
 0.000 0.001 0.001 0.007 0.015 0.016 0.004
 0.000 0.000 0.000 0.001 0.002 0.010 0.022 0.020 0.005
 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.015 0.032 0.025 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.006 0.024 0.046 0.029 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.009 0.036 0.065 0.034 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.006 0.015 0.055 0.090 0.037 0.004
 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 0.009 0.025 0.082 0.121 0.038 0.004

sum of density on p0-p1 =   1.000000
