
seed used = 140030553

K12                                  ATG GAA ACC CTC AAC GAC AAT TTA AAA GTG GTC GAA AAA GCC GAT AAC GCG GCG CAA GTC AAA GAC GCG TTA ACG AAG ATG CGC GCC GCA GCG CTG GAT GCG CAA AAA GCA ACG CCG CCG AAG CTC GAA GAT AAA TCA CCG GAC AGC CCG GAA ATG AAA GAT TTC CGC CAC GGT TTC GAC ATT CTG GTC GGT CAG ATT GAC GAC GCG CTG AAG CTG GCA AAT GAA GGT AAA GTA AAA GAA GCG CAG GCT GCT GCA GAG 
Shig4337                             ATG GAA ACC CTC AAC GAC AAT TTA AAA GTG ATC GAA AAA GCG GAT AAC GCG GCG CAA GTC AAA GAC GCG TTA ACG AAG ATG CGC GCC GCA GCG CTG GAT GCG CAA AAA GCA ACG CCG CCG AAG CTC GAA GAT AAA TCA CCG GAC AGC CCG GAA ATG AAA GAT TTC CGC CAC GGT TTC GAC ATT CTG GTC GGT CAG ATT GAC GAC GCG CTG AAG CTG GCA AAT GAA GGT AAA AAG AAG CGC AGG CTG CTG CAG AGC AAC 
CFT073                               ATG GAA ACC CTC AAC GAC AAT TTA AAA GTG GTC GAA AAA GCC GAT AAC GCG GTG CAA GTC AAA GAC GCG TTA ACT AAA ATG CGC GCT GCG GCG CTG GAT GCG CAA AAA GCG ACG CCG CCG AAG CTT GAA GGC AAA TCA CCG GAC AGC CCG GAA ATG AAA GAC TTC CGC CAC GGT TTC GAC ATT CTG GTC GGT CAG ATT GAC GAC GCG CTG AAG CTG GCA AAT GAA GGT AAA GTA AAA GAA GCG CAG GCT GCC GCA GAG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4236.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 86
# site patterns = 46
    3    5    1    1    2    6    2    2    7    1    1    1    2    5    1
    2    2    1    1    2    1    2    4    1    4    2    1    1    1    1
    1    2    1    3    2    1    1    1    1    1    1    1    1    1    1
    1

1       
K12                   ATG GAA ACC CTC AAC GAC AAT TTA AAA GTG GTC GCC GAT GCG GCG CAA GTC ACG AAG CGC GCC GCA CTG ACG CCG AAG CTC GAT TCA AGC GAT TTC CAC GGT ATT CAG GCA GTA AAA GAA GCG CAG GCT GCT GCA GAG 
Shig4337              ... ... ... ... ... ... ... ... ... ... A.. ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... AAG ..G CGC AG. .T. CTG CAG AGC A.C 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ..T ..A ... ..T ..G ... ... ... ... ..T .GC ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... 

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

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

#1: K12            
position  1:    T:0.05814    C:0.19767    A:0.27907    G:0.46512
position  2:    T:0.23256    C:0.26744    A:0.43023    G:0.06977
position  3:    T:0.15116    C:0.25581    A:0.27907    G:0.31395

#2: Shig4337       
position  1:    T:0.05814    C:0.23256    A:0.33721    G:0.37209
position  2:    T:0.24419    C:0.22093    A:0.43023    G:0.10465
position  3:    T:0.12791    C:0.27907    A:0.23256    G:0.36047

#3: CFT073         
position  1:    T:0.05814    C:0.19767    A:0.27907    G:0.46512
position  2:    T:0.24419    C:0.25581    A:0.41860    G:0.08140
position  3:    T:0.15116    C:0.26744    A:0.26744    G:0.31395

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       0 | Ser S TCT       0 | Tyr Y TAT       0 | Cys C TGT       0
      TTC       6 |       TCC       0 |       TAC       0 |       TGC       0
Leu L TTA       6 |       TCA       3 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       0 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       1 | Pro P CCT       0 | His H CAT       0 | Arg R CGT       0
      CTC       5 |       CCC       0 |       CAC       3 |       CGC       7
      CTA       0 |       CCA       0 | Gln Q CAA       6 |       CGA       0
      CTG      14 |       CCG      12 |       CAG       6 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       6 | Thr T ACT       1 | Asn N AAT       6 | Ser S AGT       0
      ATC       1 |       ACC       3 |       AAC       7 |       AGC       4
      ATA       0 |       ACA       0 | Lys K AAA      24 | Arg R AGA       0
Met M ATG       9 |       ACG       5 |       AAG      10 |       AGG       1
------------------------------------------------------------------------------
Val V GTT       0 | Ala A GCT       4 | Asp D GAT      10 | Gly G GGT       9
      GTC       8 |       GCC       5 |       GAC      19 |       GGC       1
      GTA       2 |       GCA       9 | Glu E GAA      17 |       GGA       0
      GTG       4 |       GCG      22 |       GAG       2 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.05814    C:0.20930    A:0.29845    G:0.43411
position  2:    T:0.24031    C:0.24806    A:0.42636    G:0.08527
position  3:    T:0.14341    C:0.26744    A:0.25969    G:0.32946

Codon frequencies under model, for use in evolver:
  0.00203602  0.00379691  0.00368685  0.00467735
  0.00210170  0.00391939  0.00380578  0.00482823
  0.00361230  0.00673645  0.00000000  0.00000000
  0.00072246  0.00134729  0.00000000  0.00165970
  0.00732968  0.01366886  0.01327266  0.01683845
  0.00756612  0.01410979  0.01370081  0.01738163
  0.01300427  0.02425121  0.02354827  0.02987468
  0.00260085  0.00485024  0.00470965  0.00597494
  0.01045158  0.01949079  0.01892583  0.02401039
  0.01078873  0.02011952  0.01953635  0.02478492
  0.01854313  0.03458043  0.03357809  0.04259907
  0.00370863  0.00691609  0.00671562  0.00851981
  0.01520230  0.02835023  0.02752849  0.03492420
  0.01569270  0.02926476  0.02841650  0.03605079
  0.02697182  0.05029880  0.04884086  0.06196229
  0.00539436  0.01005976  0.00976817  0.01239246



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             0.9191 (0.0931 0.1013)
CFT073               0.0590 (0.0101 0.1712) 0.3788 (0.1047 0.2763)


TREE #  1:  ((1, 2), 3);   MP score: 21
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -463.706849     +0.000000
   4..5     5..1     5..2     4..3  
  0.01623  0.00000  0.42992  0.14151  2.54296  0.84591  0.01263  0.00000  6.77694
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.58766

((1: 0.000004, 2: 0.429918): 0.016230, 3: 0.141510);

((K12: 0.000004, Shig4337: 0.429918): 0.016230, CFT073: 0.141510);

Detailed output identifying parameters

kappa (ts/tv) =  2.54296


dN/dS for site classes (K=3)

p:   0.84591  0.01263  0.14146
w:   0.00000  1.00000  6.77694

dN & dS for each branch

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

   4..5       0.016     72.2    185.8   0.9713   0.0054   0.0055    0.4    1.0
   5..1       0.000     72.2    185.8   0.9713   0.0000   0.0000    0.0    0.0
   5..2       0.430     72.2    185.8   0.9713   0.1421   0.1463   10.6   26.4
   4..3       0.142     72.2    185.8   0.9713   0.0468   0.0482    3.5    8.7


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

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

    11 V      0.917         6.296
    18 A      0.915         6.285
    44 D      0.925         6.343
    78 V      0.990*        6.719
    80 E      0.998**       6.764
    81 A      0.990*        6.717
    82 Q      0.942         6.443
    83 A      0.995**       6.747
    84 A      0.997**       6.762
    85 A      0.998**       6.764
    86 E      0.970*        6.603


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

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

    78 V      0.883         7.111 +- 2.897
    80 E      0.972*        7.763 +- 2.227
    81 A      0.875         7.036 +- 2.940
    83 A      0.940         7.545 +- 2.510
    84 A      0.969*        7.745 +- 2.258
    85 A      0.972*        7.769 +- 2.228
    86 E      0.715         5.829 +- 3.526



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:   0.757  0.197  0.038  0.007  0.001  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.005  0.022  0.055  0.096  0.133  0.160  0.175  0.179  0.175

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 0.002 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.009 0.006
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.025 0.036 0.015
 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 0.027 0.111 0.102 0.021
 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 0.022 0.118 0.313 0.160 0.013

sum of density on p0-p1 =   1.000000
