
seed used = 139989113

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0255.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 116
# site patterns = 78
    4    8    1    2    1    1    2    2    1    1    5    3    3    4    1
    2    1    1    2    1    1    1    1    3    1    2    1    2    1    2
    1    1    1    1    1    2    2    1    1    1    3    1    1    1    1
    1    2    1    1    1    1    1    1    1    1    1    1    1    1    2
    1    1    1    1    1    1    2    1    1    1    1    1    1    1    1
    1    1    1

K12                                  ATG AAA AGA AAT TTC AGC GCA GAG TTT CGC GAA TCC GCT CAA CTG GTC GTT GAC CAG AAC TAC ACC GTG GAT GCA GCC AGC GGC CTT ACA ACG CGA TGG GTG TTA CGT GAA CGG CCA CCC ATT ACC CCG ATC CTC AGG AAG CTA CGT ATA TTA ACT GTA GAT TCA ATT GGT CAA CGC AAC AGT TAT GTG AAA ACA TGG GGT TGC GGA TTT TTG AAT GAG ACG ATT TAC AGC AGA 
S2457T                               ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ..A ... ..G ... ... ..C ... .AA ... ... ... ..A A.. ... ..C C.G ... ..G ..T ... ... ... ... ... ... ... ... ... ... ..C ... ... ..C .CG CTC .TG ..G TCA G.C TC. --- --- --- --- --- --- --- --- --- --- --- C.. ..C AGT --- --- --- TCT C.. 
Shig4337                             ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ..A ... ..G ... ... ..C ... .AA ... ... ... ..A A.. ... ..C C.G ... ..G ..T ... ... ... ... ... ... ... ... ... ... ..C ... ... ..C .CG CTC .TG ..G TCA G.C TC. --- --- --- --- --- --- --- --- --- --- --- C.. ..C AGT --- --- --- TCT C.. 



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

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

#1: K12            
position  1:    T:0.13793    C:0.18103    A:0.37069    G:0.31034
position  2:    T:0.24138    C:0.19828    A:0.36207    G:0.19828
position  3:    T:0.24138    C:0.23276    A:0.32759    G:0.19828

#2: S2457T         
position  1:    T:0.12000    C:0.22000    A:0.36000    G:0.30000
position  2:    T:0.26000    C:0.24000    A:0.36000    G:0.14000
position  3:    T:0.22000    C:0.23000    A:0.32000    G:0.23000

#3: Shig4337       
position  1:    T:0.12000    C:0.22000    A:0.36000    G:0.30000
position  2:    T:0.26000    C:0.24000    A:0.36000    G:0.14000
position  3:    T:0.22000    C:0.23000    A:0.32000    G:0.23000

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       6 | Ser S TCT       2 | Tyr Y TAT       1 | Cys C TGT       0
      TTC       1 |       TCC      11 |       TAC       4 |       TGC       1
Leu L TTA       4 |       TCA       3 | *** * TAA       0 | *** * TGA       0
      TTG       3 |       TCG       0 |       TAG       0 | Trp W TGG       4
------------------------------------------------------------------------------
Leu L CTT       3 | Pro P CCT       0 | His H CAT       0 | Arg R CGT       9
      CTC       5 |       CCC       3 |       CAC       0 |       CGC       6
      CTA       3 |       CCA       3 | Gln Q CAA      13 |       CGA       3
      CTG       7 |       CCG       3 |       CAG       6 |       CGG       1
------------------------------------------------------------------------------
Ile I ATT      11 | Thr T ACT       1 | Asn N AAT       7 | Ser S AGT       3
      ATC       3 |       ACC       6 |       AAC       5 |       AGC       5
      ATA       3 |       ACA       9 | Lys K AAA      29 | Arg R AGA       6
Met M ATG      14 |       ACG       4 |       AAG       6 |       AGG       3
------------------------------------------------------------------------------
Val V GTT       7 | Ala A GCT       9 | Asp D GAT      10 | Gly G GGT       3
      GTC       4 |       GCC       8 |       GAC       5 |       GGC       6
      GTA       1 |       GCA       7 | Glu E GAA      17 |       GGA       1
      GTG       5 |       GCG       2 |       GAG      11 |       GGG       0
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.12658    C:0.20570    A:0.36392    G:0.30380
position  2:    T:0.25316    C:0.22468    A:0.36076    G:0.16139
position  3:    T:0.22785    C:0.23101    A:0.32278    G:0.21835

Codon frequencies under model, for use in evolver:
  0.00753763  0.00764231  0.01067830  0.00722356
  0.00668964  0.00678255  0.00947699  0.00641091
  0.01074112  0.01089030  0.00000000  0.00000000
  0.00480524  0.00487198  0.00000000  0.00460502
  0.01224864  0.01241876  0.01735224  0.01173828
  0.01087067  0.01102165  0.01540011  0.01041772
  0.01745431  0.01769673  0.02472694  0.01672705
  0.00780851  0.00791696  0.01106205  0.00748315
  0.02167067  0.02197165  0.03070012  0.02076773
  0.01923272  0.01949984  0.02724636  0.01843136
  0.03088071  0.03130961  0.04374767  0.02959401
  0.01381505  0.01400693  0.01957133  0.01323943
  0.01809030  0.01834155  0.02562793  0.01733654
  0.01605514  0.01627813  0.02274478  0.01538618
  0.02577868  0.02613672  0.03651979  0.02470457
  0.01153257  0.01169274  0.01633780  0.01105204



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               0.1893 (0.0859 0.4540)
Shig4337             0.1893 (0.0859 0.4540)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -603.683016     +0.000000
   4..1     4..5     5..2     5..3  
  7.24197  7.98252  0.00000  0.00000  1.62562  0.89044  0.00000  0.01096 171.86159
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  15.22450

(1: 7.241968, (2: 0.000004, 3: 0.000004): 7.982525);

(K12: 7.241968, (S2457T: 0.000004, Shig4337: 0.000004): 7.982525);

Detailed output identifying parameters

kappa (ts/tv) =  1.62562


dN/dS for site classes (K=3)

p:   0.89044  0.00000  0.10956
w:   0.01096  1.00000171.86159

dN & dS for each branch

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

   4..1       7.242     85.0    263.0  18.8382   3.1402   0.1667   14.2  825.9
   4..5       7.983     85.0    263.0  18.8382   3.4613   0.1837   15.6  910.4
   5..2       0.000     85.0    263.0  18.8382   0.0000   0.0000    0.0    0.0
   5..3       0.000     85.0    263.0  18.8382   0.0000   0.0000    0.0    0.0


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

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

    22 N      0.681         117.035
    30 S      0.999**       171.666
    89 V      0.909         156.308
    90 D      1.000**       171.851
    91 S      0.954*        163.936
    92 I      0.671         115.292
    93 G      1.000**       171.858
    94 Q      0.999**       171.735
    95 R      1.000**       171.809
   110 E      1.000**       171.860
   115 S      1.000**       171.856


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

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

    30 S      0.727         6.487 +- 3.751
    90 D      0.935         8.120 +- 2.560
    91 S      0.564         5.072 +- 4.245
    93 G      0.971*        8.394 +- 2.177
    94 Q      0.773         6.852 +- 3.582
    95 R      0.920         7.989 +- 2.696
   110 E      0.932         8.084 +- 2.584
   115 S      0.953*        8.259 +- 2.379



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:   0.986  0.014  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.003  0.012  0.029  0.055  0.090  0.131  0.177  0.226  0.275

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 0.001 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.016 0.036 0.037
 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 0.036 0.393 0.389 0.083

sum of density on p0-p1 =   1.000000
