
seed used = 139992869

K12                                  ATG GGA CAC AAG CCC TTA TAC CGG CAG ATT GCC GAT CGC ATT CGT GAA CAA ATT GCG CGT GGC GAG CTT AAA CCT GGC GAT GCG TTA CCC ACT GAA TCA GCG CTA CAA ACA GAG TTT GGC GTC AGC CGG GTT ACG GTG CGT CAG GCT TTG CGC CAG CTA GTC GAG CAG CAG ATC CTC GAA AGC ATT CAG GGC AGC GGG ACT TAC GTC AAA GAA GAG CGG GTC AAT TAC GAT ATT TTT CAG TTA ACC AGT TTT GAT GAA AAA CTG TCG GAC CGT CAC GTC GAT ACA CAC AGT GAA GTT CTG ATA TTC GAA GTG ATT CCG GCT GAC GAT TTT CTT CAG CAA CAG CTA CAA ATC ACC CCG CAG GAT CGT GTG TGG CAT GTG AAG CGC GTG CGC TAT CGC AAG CAA AAG CCA ATG GCG CTG GAA GAA ACC TGG ATG CCG CTT GCG TTG TTC CCG GAT CTC ACC TGG CAG GTC ATG GAA AAT TCG AAA TAT CAC TTT ATC GAA GAA GTG AAG AAA ATG GTT ATC GAT CGT AGC GAA CAG GAA ATC ATT CCT CTG ATG CCA ACC GAA GAG ATG AGC CGT CTG CTT AAT ATC AGC CAG ACA AAG CCG ATT CTT GAA AAA GTA TCG CGT GGA TAT TTA GTT GAT GGT CGG GTG TTT GAA TAT AGC CGC AAC GCT TTT AAT ACC GAT GAC TAT AAA TTT ACC CTG ATA GCG CAG CGA AAA --- --- --- --- TCA TCG CGA 
S2457T                               ATG GGA CAC AAA CCC TTA TAC CGA CAG ATT GCT GAT CGC ATT CGT GAG CAA ATT GCG CGT GGC GAG CTT AAA CCT GGC GAT GCG TTA CCT ACC GAA TCG GCA TTA CAA ACA GAG TTT GGC GTC AGC CGG GTT ACG GTG CGT CAG GCT TTG CGC CAG TTA GTC GAG CAA CAG ATC CTC GAA AGC ATT CAG GGC AGC GGG ACT TAC GTC AAA GAA GAG CGG GTC AAT TAC GAT ATT TTT CAG TTA ACC AGT TTT GAT GAA AAA CTG TCG GAC CGT CAC GTC GAT ACA CAC AGT GAA GTT CTG ATA TTT GAA GTG ATT CCG GCT GAC GAT TTT CTT CAG CAA CAG CTA CAA ATC ACC GTG CAG GAT CGT GTG TGG CAT GTG AAG CGC GTG CGC TAT CGC AAG CAA AAG CCA ATG GCG CTG GAA GAA ACC TGG ATG CCG CTT GCG TTG TTC CCG GAT CTC ACC TGG CAG GTC ATG GAA AAT TCG AAA TAT CAC TTT ATT GAA GAA GTG AAG AAG ATG GTT ATC GAT CGT AGC GAA CAG GAA ATC ATT CCT CTG ATG CCA ACC GAA GAG ATG AGC CGT CTG CTT AAT ATC AGC CAG ACA AAG CCG ATT CTT GAA AAA GTA TCG CGT GGA TAT TTA GTT GAT GGT CGG GTG TTT GAA TAT AGC CGC AAC GCT TTT AAT ACC GAT GAC TAT AAA TTT ACC CTG ATA GCG CAG CCG AAA ATC ATC GCG ATA AGC ACA AAA 
Shig4337                             ATG GGA CAC AAA CCC TTA TAC CGA CAG ATT GCT GAT CGC ATT CGT GAG CAA ATT GCG CGT GGC GAG CTT AAA CCT GGC GAT GCG TTA CCT ACC GAA TCG GCA TTA CAA ACA GAG TTT GGC GTC AGC CGG GTT ACG GTG CGT CAG GCT TTG CGC CAG TTA GTC GAG CAA CAG ATC CTC GAA AGC ATT CAG GGC AGC GGG ACT TAC GTC AAA GAA GAG CGG GTC AAT TAC GAT ATT TTT CAG TTA ACC AGT TTT GAT GAA AAA CTG TCG GAC CGT CAC GTC GAT ACA CAC AGT GAA GTT CTG ATA TTT GAA GTG ATT CCG GCT GAC GAT TTT CTT CAG CAA CAG CTA CAA ATC ACC GTG CAG GAT CGT GTG TGG CAT GTG AAG CGC GTG CGC TAT CGC AAG CAA AAG CCA ATG GCG CTG GAA GAA ACC TGG ATG CCG CTT GCG TTG TTC CCG GAT CTC ACC TGG CAG GTC ATG GAA AAT TCG AAA TAT CAC TTT ATT GAA GAA GTG AAG AAG ATG GTT ATC GAT CGT AGC GAA CAG GAA ATC ATT CCT CTG ATG CCA ACC GAA GAG ATG AGC CGT CTG CTT AAT ATC AGC CAG ACA AAG CCG ATT CTT GAA AAA GTA TCG CGT GGA TAT TTA GTT GAT GGT CGG GTG TTT GAA TAT AGC CGC AAC GCT TTT AAT ACC GAT GAC TAT AAA TTT ACC CTG ATA GCG CAG CGA AAA --- --- --- --- TCA TCG CGA 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0730.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 244
# site patterns = 72
    7    2    4    1    1    4    3    1   13    8    1   11    6    8    1
    5    5    4    5    5    7    2    1    1   16    1    1    2    3    8
    6    7    3    4    1    7    3    2    1    5    2    1    1    4    7
    2    6    3    3    2    1    4    1    1    3    1    5    5    2    1
    1    1    1    1    1    1    2    1    1    1    1    1

K12                                  ATG GGA CAC AAG CCC TTA TAC CGG CAG ATT GCC GAT CGC CGT GAA CAA GCG GGC GAG CTT AAA CCT CCC ACT GAA TCA GCG CTA ACA TTT GTC AGC CGG GTT ACG GTG GCT TTG CAG ATC CTC GGG ACT AAT ACC AGT CTG TCG GAC ATA TTC CCG CTA CCG TGG CAT AAG TAT CCA TTC ATC AAA GTA GGT AAC CGA --- --- --- TCA TCG CGA 
S2457T                               ... ... ... ..A ... ... ... ..A ... ... ..T ... ... ... ..G ... ... ... ... ... ... ... ..T ..C ... ..G ..A T.. ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T ... ... GT. ... ... ... ... ... ... ..T ..G ... ... ... .CG ATC GCG ATA AGC A.A AA. 
Shig4337                             ... ... ... ..A ... ... ... ..A ... ... ..T ... ... ... ..G ... ... ... ... ... ... ... ..T ..C ... ..G ..A T.. ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T ... ... GT. ... ... ... ... ... ... ..T ..G ... ... ... ... --- --- --- ... ... ... 



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

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

#1: K12            
position  1:    T:0.13750    C:0.29583    A:0.26667    G:0.30000
position  2:    T:0.30417    C:0.16667    A:0.36250    G:0.16667
position  3:    T:0.26667    C:0.22500    A:0.21250    G:0.29583

#2: S2457T         
position  1:    T:0.13525    C:0.27459    A:0.28689    G:0.30328
position  2:    T:0.31557    C:0.16393    A:0.36066    G:0.15984
position  3:    T:0.27459    C:0.22131    A:0.21311    G:0.29098

#3: Shig4337       
position  1:    T:0.14583    C:0.28333    A:0.26667    G:0.30417
position  2:    T:0.30833    C:0.16250    A:0.36250    G:0.16667
position  3:    T:0.27917    C:0.21250    A:0.21667    G:0.29167

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      26 | Ser S TCT       0 | Tyr Y TAT      15 | Cys C TGT       0
      TTC       4 |       TCC       0 |       TAC       9 |       TGC       0
Leu L TTA      16 |       TCA       3 | *** * TAA       0 | *** * TGA       0
      TTG       6 |       TCG      13 |       TAG       0 | Trp W TGG       9
------------------------------------------------------------------------------
Leu L CTT      15 | Pro P CCT       8 | His H CAT       3 | Arg R CGT      24
      CTC       6 |       CCC       4 |       CAC      12 |       CGC      18
      CTA       5 |       CCA       6 | Gln Q CAA      17 |       CGA       6
      CTG      18 |       CCG      14 |       CAG      40 |       CGG      10
------------------------------------------------------------------------------
Ile I ATT      26 | Thr T ACT       4 | Asn N AAT      12 | Ser S AGT       6
      ATC      18 |       ACC      23 |       AAC       3 |       AGC      22
      ATA       7 |       ACA      10 | Lys K AAA      25 | Arg R AGA       0
Met M ATG      21 |       ACG       3 |       AAG      18 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      12 | Ala A GCT      11 | Asp D GAT      33 | Gly G GGT       3
      GTC      18 |       GCC       1 |       GAC       9 |       GGC      12
      GTA       3 |       GCA       2 | Glu E GAA      49 |       GGA       6
      GTG      23 |       GCG      17 |       GAG      17 |       GGG       3
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13950    C:0.28453    A:0.27348    G:0.30249
position  2:    T:0.30939    C:0.16436    A:0.36188    G:0.16436
position  3:    T:0.27348    C:0.21961    A:0.21409    G:0.29282

Codon frequencies under model, for use in evolver:
  0.01217505  0.00977693  0.00953097  0.01303591
  0.00646799  0.00519400  0.00506333  0.00692533
  0.01424046  0.01143552  0.00000000  0.00000000
  0.00646799  0.00519400  0.00000000  0.00692533
  0.02483227  0.01994107  0.01943941  0.02658809
  0.01319215  0.01059369  0.01032718  0.01412492
  0.02904489  0.02332393  0.02273716  0.03109857
  0.01319215  0.01059369  0.01032718  0.01412492
  0.02386791  0.01916666  0.01868448  0.02555554
  0.01267983  0.01018229  0.00992613  0.01357638
  0.02791694  0.02241815  0.02185417  0.02989086
  0.01267983  0.01018229  0.00992613  0.01357638
  0.02639936  0.02119949  0.02066617  0.02826598
  0.01402466  0.01126223  0.01097890  0.01501630
  0.03087782  0.02479583  0.02417203  0.03306110
  0.01402466  0.01126223  0.01097890  0.01501630



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                 
S2457T               0.1229 (0.0140 0.1142)
Shig4337             0.0398 (0.0036 0.0906) 0.5113 (0.0104 0.0203)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1107.046806     +0.000000
   4..1     4..5     5..2     5..3  
  0.61186  0.65611  0.60812  0.00000 99.00000  0.97868  0.00000  0.00000 778.59696
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.87609

(1: 0.611861, (2: 0.608123, 3: 0.000004): 0.656105);

(K12: 0.611861, (S2457T: 0.608123, Shig4337: 0.000004): 0.656105);

Detailed output identifying parameters

kappa (ts/tv) = 99.00000


dN/dS for site classes (K=3)

p:   0.97868  0.00000  0.02132
w:   0.00000  1.00000778.59696

dN & dS for each branch

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

   4..1       0.612    268.8    463.2  16.5989   0.3114   0.0188    5.0  144.3
   4..5       0.656    268.8    463.2  16.5989   0.3340   0.0201    5.4  154.7
   5..2       0.608    268.8    463.2  16.5989   0.3095   0.0186    5.0  143.4
   5..3       0.000    268.8    463.2  16.5989   0.0000   0.0000    0.0    0.0


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

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

   119 P      1.000**       778.597
   236 R      1.000**       778.596
   242 S      1.000**       778.597
   243 S      1.000**       778.597
   244 R      1.000**       778.597


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

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

   119 P      0.952*        8.563 +- 2.376
   236 R      0.659         6.108 +- 4.243
   242 S      0.989*        8.843 +- 1.880
   243 S      0.612         5.697 +- 4.337
   244 R      0.934         8.422 +- 2.603



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:   0.827  0.145  0.024  0.004  0.001  0.000  0.000  0.000  0.000  0.000
w2:   0.002  0.004  0.009  0.020  0.038  0.066  0.108  0.166  0.243  0.343

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005
 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 0.028
 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 0.019 0.148
 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 0.004 0.114 0.676

sum of density on p0-p1 =   1.000000
