
seed used = 139998797

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1377.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 298
# site patterns = 84
    7   11    1    3    9   11    1    3    4    2    5    1    1   15    4
    4   11    4   11   12   10   15   14   14    9    6    4    6    7    3
    1    5    9    4    1    7    8    5    1    1    1    4    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                   ATG AAA AGC GTA CTG GCA CTT TTA ATT CCT GCC CTC GCC GGT GCT CAT GAA GTT TAT AAT GAC GGC AAC GAT TTT TCT TCA GCG CAG AGC GCG CGT ACC CAA CTC ACT TAC TGG ACT AAA GGG TTC GGA ATC ACC CTG CGA GTC GTG GGA AGT AAC GGA CGT CGC CTT TCC ACA CGC GCG GGG CTA CTG ACG CCG GCT GTG GCA AAT GTC GCA CAG TAC CAG TTT GAT TTT GGT CTG CGT CCG GCA GTC TCT 
Shig4337              ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ..T .A. ..C ..T ... ... ... ... ... ... ... ..A ... ... ..A ..T ..G ..C ..T AGT ACC AGT TT. A.. TT. G.C T.C G.C ..G .A. T.T C.T ..C 
CFT073                ... ... ... ... ... ... ..C ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ..C .C. ..A ... ... ... ..T ..A ..T ... ... ..T ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ..T ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 11 10 11 | Ser TCT  7  7  7 | Tyr TAT 11 11 11 | Cys TGT  0  0  0
    TTC  4  4  4 |     TCC  1  2  1 |     TAC  9  8  9 |     TGC  0  1  0
Leu TTA  3  3  3 |     TCA  4  4  4 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  0  1  0 |     TCG  0  0  0 |     TAG  0  0  0 | Trp TGG  5  5  5
--------------------------------------------------------------------------
Leu CTT  2  4  1 | Pro CCT  2  2  2 | His CAT  4  4  4 | Arg CGT  7  6  8
    CTC  2  1  3 |     CCC  0  0  0 |     CAC  0  0  0 |     CGC  2  2  2
    CTA  1  2  2 |     CCA  0  0  0 | Gln CAA  4  4  4 |     CGA  1  1  0
    CTG 12 10 11 |     CCG  2  1  2 |     CAG  9  8  9 |     CGG  0  1  0
--------------------------------------------------------------------------
Ile ATT  4  5  4 | Thr ACT  8  8  8 | Asn AAT 13 13 12 | Ser AGT  1  3  1
    ATC  1  1  1 |     ACC 10 11 10 |     AAC 15 15 16 |     AGC  4  3  4
    ATA  0  0  0 |     ACA  2  2  3 | Lys AAA 12 12 11 | Arg AGA  0  1  0
Met ATG  7  7  7 |     ACG  1  1  1 |     AAG  0  0  0 |     AGG  0  0  0
--------------------------------------------------------------------------
Val GTT  4  6  5 | Ala GCT  5  4  7 | Asp GAT 15 14 15 | Gly GGT 16 15 17
    GTC  3  3  3 |     GCC  6  6  5 |     GAC 10 10 10 |     GGC 15 15 15
    GTA  3  3  3 |     GCA 14 12 15 | Glu GAA 11 12 11 |     GGA  3  3  3
    GTG  2  1  1 |     GCG  8  9  6 |     GAG  0  0  0 |     GGG  2  1  1
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.18456    C:0.16107    A:0.26174    G:0.39262
position  2:    T:0.19799    C:0.23490    A:0.37919    G:0.18792
position  3:    T:0.36913    C:0.27517    A:0.19463    G:0.16107

#2: Shig4337       
position  1:    T:0.18792    C:0.15436    A:0.27517    G:0.38255
position  2:    T:0.20470    C:0.23154    A:0.37248    G:0.19128
position  3:    T:0.37584    C:0.27517    A:0.19799    G:0.15101

#3: CFT073         
position  1:    T:0.18456    C:0.16107    A:0.26174    G:0.39262
position  2:    T:0.19799    C:0.23826    A:0.37584    G:0.18792
position  3:    T:0.37919    C:0.27852    A:0.19799    G:0.14430

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      32 | Ser S TCT      21 | Tyr Y TAT      33 | Cys C TGT       0
      TTC      12 |       TCC       4 |       TAC      26 |       TGC       1
Leu L TTA       9 |       TCA      12 | *** * TAA       0 | *** * TGA       0
      TTG       1 |       TCG       0 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT       7 | Pro P CCT       6 | His H CAT      12 | Arg R CGT      21
      CTC       6 |       CCC       0 |       CAC       0 |       CGC       6
      CTA       5 |       CCA       0 | Gln Q CAA      12 |       CGA       2
      CTG      33 |       CCG       5 |       CAG      26 |       CGG       1
------------------------------------------------------------------------------
Ile I ATT      13 | Thr T ACT      24 | Asn N AAT      38 | Ser S AGT       5
      ATC       3 |       ACC      31 |       AAC      46 |       AGC      11
      ATA       0 |       ACA       7 | Lys K AAA      35 | Arg R AGA       1
Met M ATG      21 |       ACG       3 |       AAG       0 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      15 | Ala A GCT      16 | Asp D GAT      44 | Gly G GGT      48
      GTC       9 |       GCC      17 |       GAC      30 |       GGC      45
      GTA       9 |       GCA      41 | Glu E GAA      34 |       GGA       9
      GTG       4 |       GCG      23 |       GAG       0 |       GGG       4
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.18568    C:0.15884    A:0.26622    G:0.38926
position  2:    T:0.20022    C:0.23490    A:0.37584    G:0.18904
position  3:    T:0.37472    C:0.27629    A:0.19687    G:0.15213

Codon frequencies under model, for use in evolver:
  0.01438098  0.01060329  0.00755538  0.00583825
  0.01687154  0.01243962  0.00886386  0.00684934
  0.02699447  0.01990338  0.00000000  0.00000000
  0.01357757  0.01001093  0.00000000  0.00551209
  0.01230180  0.00907029  0.00646304  0.00499417
  0.01443228  0.01064112  0.00758233  0.00585908
  0.02309165  0.01702579  0.01213173  0.00937452
  0.01161455  0.00856357  0.00610197  0.00471516
  0.02061852  0.01520231  0.01083241  0.00837050
  0.02418932  0.01783511  0.01270842  0.00982014
  0.03870291  0.02853618  0.02033347  0.01571223
  0.01946664  0.01435302  0.01022725  0.00790288
  0.03014808  0.02222859  0.01583899  0.01223922
  0.03536926  0.02607823  0.01858206  0.01435886
  0.05659081  0.04172517  0.02973129  0.02297418
  0.02846383  0.02098677  0.01495413  0.01155547



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             0.2545 (0.0279 0.1098)
CFT073               0.0242 (0.0015 0.0602) 0.2045 (0.0295 0.1440)


TREE #  1:  ((1, 2), 3);   MP score: 37
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1443.724423     +0.000000
   4..5     5..1     5..2     4..3  
  0.02066  0.01097  0.20571  0.02358  1.18378  0.87824  0.09765  0.00000 15.34242
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.26091

((1: 0.010967, 2: 0.205706): 0.020665, 3: 0.023575);

((K12: 0.010967, Shig4337: 0.205706): 0.020665, CFT073: 0.023575);

Detailed output identifying parameters

kappa (ts/tv) =  1.18378


dN/dS for site classes (K=3)

p:   0.87824  0.09765  0.02411
w:   0.00000  1.00000 15.34242

dN & dS for each branch

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

   4..5       0.021    198.6    695.4   0.4676   0.0055   0.0118    2.3    3.8
   5..1       0.011    198.6    695.4   0.4676   0.0029   0.0062    1.2    2.0
   5..2       0.206    198.6    695.4   0.4676   0.0547   0.1170   23.2   38.1
   4..3       0.024    198.6    695.4   0.4676   0.0063   0.0134    2.7    4.4


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

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

   285 A      0.944         14.533
   286 Q      0.979*        15.041
   287 Y      0.867         13.438
   288 Q      0.869         13.466
   290 D      0.568         9.150
   293 L      0.593         9.500


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

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

   285 A      0.962*        8.012 +- 2.343
   286 Q      0.985*        8.166 +- 2.100
   287 Y      0.927         7.760 +- 2.658
   288 Q      0.816         6.939 +- 3.505
   290 D      0.842         7.104 +- 3.210
   293 L      0.584         5.074 +- 4.170
   295 P      0.501         4.358 +- 4.144



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:   0.971  0.029  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.002  0.007  0.019  0.042  0.073  0.109  0.144  0.177  0.204  0.224

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 0.001 0.072
 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 0.042 0.883

sum of density on p0-p1 =   1.000000
