
seed used = 140021577

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3557.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 183
# site patterns = 77
    1    1    1    1   12    1    1    2    1    1    1    1    1    1    1
    1    1    1    4    6    8    4    3    2    3    2    1    1    1    5
    6    4    3    1    4    2    3    3    3    2    3    1    1    2    4
    3    2    3    2    2    3    5    1    1    2    8    2    5    2    5
    3    1    1    1    3    1    2    1    1    1    1    3    1    1    2
    1    1

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



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

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

#1: K12            
position  1:    T:0.14451    C:0.22543    A:0.28324    G:0.34682
position  2:    T:0.27746    C:0.22543    A:0.32948    G:0.16763
position  3:    T:0.30636    C:0.19653    A:0.27168    G:0.22543

#2: S2457T         
position  1:    T:0.14451    C:0.22543    A:0.28324    G:0.34682
position  2:    T:0.27746    C:0.22543    A:0.32948    G:0.16763
position  3:    T:0.31214    C:0.19653    A:0.26590    G:0.22543

#3: Shig4337       
position  1:    T:0.15934    C:0.22527    A:0.28571    G:0.32967
position  2:    T:0.26923    C:0.23626    A:0.31868    G:0.17582
position  3:    T:0.30769    C:0.19780    A:0.28022    G:0.21429

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      11 | Ser S TCT       3 | Tyr Y TAT       9 | Cys C TGT       0
      TTC       3 |       TCC       3 |       TAC      10 |       TGC       0
Leu L TTA      10 |       TCA      14 | *** * TAA       0 | *** * TGA       0
      TTG       6 |       TCG       3 |       TAG       0 | Trp W TGG       7
------------------------------------------------------------------------------
Leu L CTT      18 | Pro P CCT       5 | His H CAT       7 | Arg R CGT       6
      CTC       6 |       CCC       9 |       CAC       9 |       CGC      12
      CTA       3 |       CCA       9 | Gln Q CAA       3 |       CGA       9
      CTG      10 |       CCG       0 |       CAG      10 |       CGG       3
------------------------------------------------------------------------------
Ile I ATT      15 | Thr T ACT       6 | Asn N AAT       6 | Ser S AGT       7
      ATC       9 |       ACC       7 |       AAC       3 |       AGC       2
      ATA       3 |       ACA       4 | Lys K AAA      37 | Arg R AGA       3
Met M ATG      11 |       ACG       6 |       AAG      19 |       AGG      12
------------------------------------------------------------------------------
Val V GTT      13 | Ala A GCT      24 | Asp D GAT      15 | Gly G GGT      18
      GTC      14 |       GCC       9 |       GAC       3 |       GGC       5
      GTA       4 |       GCA      13 | Glu E GAA      26 |       GGA       6
      GTG       9 |       GCG       6 |       GAG      15 |       GGG       0
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.14962    C:0.22538    A:0.28409    G:0.34091
position  2:    T:0.27462    C:0.22917    A:0.32576    G:0.17045
position  3:    T:0.30871    C:0.19697    A:0.27273    G:0.22159

Codon frequencies under model, for use in evolver:
  0.01309119  0.00835266  0.01156522  0.00939674
  0.01092437  0.00697015  0.00965098  0.00784142
  0.01552885  0.00990798  0.00000000  0.00000000
  0.00812556  0.00518441  0.00000000  0.00583246
  0.01971963  0.01258185  0.01742103  0.01415458
  0.01645569  0.01049934  0.01453755  0.01181176
  0.02339157  0.01492468  0.02066494  0.01679027
  0.01223977  0.00780943  0.01081305  0.00878560
  0.02485668  0.01585948  0.02195928  0.01784191
  0.02074247  0.01323446  0.01832464  0.01488877
  0.02948517  0.01881262  0.02604825  0.02116420
  0.01542829  0.00984381  0.01362990  0.01107429
  0.02982802  0.01903137  0.02635113  0.02141030
  0.02489097  0.01588135  0.02198957  0.01786652
  0.03538220  0.02257515  0.03125790  0.02539704
  0.01851394  0.01181258  0.01635588  0.01328915



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               0.0000 (0.0000 0.0079)
Shig4337             0.4660 (0.0342 0.0734) 0.5278 (0.0342 0.0648)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -830.910982     +0.000000
   4..1     4..5     5..2     5..3  
  0.00000  0.00614  0.00000  0.57634  0.82731  0.95157  0.00000  0.00000 140.94749
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.58249

(1: 0.000005, (2: 0.000004, 3: 0.576342): 0.006143);

(K12: 0.000005, (S2457T: 0.000004, Shig4337: 0.576342): 0.006143);

Detailed output identifying parameters

kappa (ts/tv) =  0.82731


dN/dS for site classes (K=3)

p:   0.95157  0.00000  0.04843
w:   0.00000  1.00000140.94749

dN & dS for each branch

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

   4..1       0.000    126.8    422.2   6.8258   0.0000   0.0000    0.0    0.0
   4..5       0.006    126.8    422.2   6.8258   0.0026   0.0004    0.0    1.1
   5..2       0.000    126.8    422.2   6.8258   0.0000   0.0000    0.0    0.0
   5..3       0.576    126.8    422.2   6.8258   0.2393   0.0351    4.4  101.0


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

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

     1 M      1.000**       140.947
     2 S      1.000**       140.947
     3 K      1.000**       140.947
     4 P      1.000**       140.947
     6 Y      1.000**       140.947
     9 F      1.000**       140.947
    10 E      1.000**       140.947
   128 G      1.000**       140.947


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

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

     1 M      0.990*        9.567 +- 1.440
     2 S      0.991**       9.581 +- 1.397
     3 K      0.915         8.909 +- 2.707
     4 P      0.921         8.959 +- 2.649
     6 Y      0.744         7.364 +- 4.054
     9 F      0.687         6.838 +- 4.285
    10 E      0.992**       9.582 +- 1.390
   128 G      0.671         6.686 +- 4.334



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:   0.523  0.251  0.119  0.056  0.027  0.013  0.006  0.003  0.002  0.001
w2:   0.000  0.000  0.001  0.003  0.009  0.024  0.057  0.126  0.262  0.520

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.001 0.001
 0.000 0.000 0.000 0.001 0.001
 0.000 0.000 0.000 0.000 0.001 0.003 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.006 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.013 0.007
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.010 0.029 0.012
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005 0.026 0.064 0.022
 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 0.014 0.067 0.135 0.035
 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 0.037 0.169 0.272 0.050

sum of density on p0-p1 =   1.000000
