
seed used = 139989125

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0258.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 244
# site patterns = 102
    3    8    3    6    2    5    2    4    2    4    2    2    9    5    3
    3    5    4    4    6    5    2    2    3    4    4    3    1    3    1
    2    3    3    1    3    1    3    1    1    2    1    1    1    1    9
    1    1    1    1    1    1    1    1    1    2    3    2    2    2    2
    2    9    3    2    3    2    1    1    1    3    5    3    4    2    2
    2    2    2    2    1    2    1    1    1    2    1    1    3    1    1
    1    2    1    1    1    1    1    1    1    1    1    1

K12                                  ATG CTG AAT GAG TTC GAT CAA TAC CAT CGC AGC GGG AAA GCC AGA CGG TGG AAC AGT ATC GGC CGA ACG GCG GTC GAA CAG CCC GTG TGC TAT TTT CTC ACC GCA GTG AGG TGT GGT AAG ACT CCC GTT GAC --- CAC CTC ATT CGT TCA CCG TCG ACA TTA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GTG CGA --- --- --- --- --- --- --- --- --- --- --- --- ATA GGG ATT CTT CTC GGC 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... A.. ... ... --- ... A.. ... ... ... ... ... ... ... TCA GGC AAC TAC AGT GAA AGC AAA GTC GAT ATG GCT CAA CTC CGA CTG TGG GCC TTC TAT CAG GTT TTT AAG ATC GAC CGT GTG C.. GCT CAC CGC ACA GGT TCC AGG TGT CCG ACG TTA ACC AAT C.C ..C ..A ..G TA. C.G 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... A.. ... ... --- ... A.. ... ... ... ... ... ... ... TCA GGC AAC TAC AGT GAA AGC AAA GTC GAT ATG GCT CAA CTC CGA CTG TGG GCC TTC TAT CAG GTT TTT AAG ATC GAC CGT GTG C.. GCT CAC CGC ACA GGT TCC AGG TGT CCG ACG TTA ACC AAT C.C ..C ..A ..G TA. C.G 



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT  3  5  5 | Ser TCT  0  0  0 | Tyr TAT  2  4  4 | Cys TGT  1  2  2
    TTC  2  6  6 |     TCC  0  1  1 |     TAC  4  7  7 |     TGC  1  1  1
Leu TTA  1  2  2 |     TCA  1  3  3 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  0  0  0 |     TCG  1  1  1 |     TAG  0  0  0 | Trp TGG  5 10 10
--------------------------------------------------------------------------
Leu CTT  1  0  0 | Pro CCT  0  0  0 | His CAT  2  2  2 | Arg CGT  1  3  3
    CTC  5  5  5 |     CCC  2  1  1 |     CAC  1  3  3 |     CGC  4  5  5
    CTA  0  0  0 |     CCA  0  0  0 | Gln CAA  2  3  3 |     CGA  3  3  3
    CTG  8 13 13 |     CCG  1  3  3 |     CAG  3  5  5 |     CGG  3  4  4
--------------------------------------------------------------------------
Ile ATT  2  1  1 | Thr ACT  1  1  1 | Asn AAT  3  4  4 | Ser AGT  4  6  6
    ATC  6  9  9 |     ACC  1  3  3 |     AAC  4  6  6 |     AGC  2  4  4
    ATA  1  1  1 |     ACA  1  2  2 | Lys AAA  9 18 18 | Arg AGA  3  3  3
Met ATG  3  6  6 |     ACG  2  3  3 |     AAG  2  4  4 |     AGG  3  4  4
--------------------------------------------------------------------------
Val GTT  1  3  3 | Ala GCT  0  3  3 | Asp GAT  5  7  7 | Gly GGT  1  4  4
    GTC  4  7  7 |     GCC  5  8  8 |     GAC  1  2  2 |     GGC  6  9  9
    GTA  0  0  0 |     GCA  3  3  3 | Glu GAA  4  6  6 |     GGA  0  0  0
    GTG  5  4  4 |     GCG  3  4  4 |     GAG  6  6  6 |     GGG  3  2  2
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13907    C:0.23841    A:0.31126    G:0.31126
position  2:    T:0.27815    C:0.13907    A:0.31788    G:0.26490
position  3:    T:0.17881    C:0.31788    A:0.18543    G:0.31788

#2: S2457T         
position  1:    T:0.17872    C:0.21277    A:0.31915    G:0.28936
position  2:    T:0.26383    C:0.15319    A:0.32766    G:0.25532
position  3:    T:0.19149    C:0.32766    A:0.18723    G:0.29362

#3: Shig4337       
position  1:    T:0.17872    C:0.21277    A:0.31915    G:0.28936
position  2:    T:0.26383    C:0.15319    A:0.32766    G:0.25532
position  3:    T:0.19149    C:0.32766    A:0.18723    G:0.29362

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      13 | Ser S TCT       0 | Tyr Y TAT      10 | Cys C TGT       5
      TTC      14 |       TCC       2 |       TAC      18 |       TGC       3
Leu L TTA       5 |       TCA       7 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       3 |       TAG       0 | Trp W TGG      25
------------------------------------------------------------------------------
Leu L CTT       1 | Pro P CCT       0 | His H CAT       6 | Arg R CGT       7
      CTC      15 |       CCC       4 |       CAC       7 |       CGC      14
      CTA       0 |       CCA       0 | Gln Q CAA       8 |       CGA       9
      CTG      34 |       CCG       7 |       CAG      13 |       CGG      11
------------------------------------------------------------------------------
Ile I ATT       4 | Thr T ACT       3 | Asn N AAT      11 | Ser S AGT      16
      ATC      24 |       ACC       7 |       AAC      16 |       AGC      10
      ATA       3 |       ACA       5 | Lys K AAA      45 | Arg R AGA       9
Met M ATG      15 |       ACG       8 |       AAG      10 |       AGG      11
------------------------------------------------------------------------------
Val V GTT       7 | Ala A GCT       6 | Asp D GAT      19 | Gly G GGT       9
      GTC      18 |       GCC      21 |       GAC       5 |       GGC      24
      GTA       0 |       GCA       9 | Glu E GAA      16 |       GGA       0
      GTG      13 |       GCG      11 |       GAG      18 |       GGG       7
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.16908    C:0.21900    A:0.31723    G:0.29469
position  2:    T:0.26731    C:0.14976    A:0.32528    G:0.25765
position  3:    T:0.18841    C:0.32528    A:0.18680    G:0.29952

Codon frequencies under model, for use in evolver:
  0.00882326  0.01523332  0.00874785  0.01402672
  0.00494315  0.00853433  0.00490090  0.00785834
  0.01073674  0.01853693  0.00000000  0.00000000
  0.00850435  0.01468272  0.00000000  0.01351973
  0.01142822  0.01973078  0.01133055  0.01816794
  0.00640256  0.01105399  0.00634784  0.01017843
  0.01390663  0.02400974  0.01378777  0.02210798
  0.01101515  0.01901762  0.01092101  0.01751127
  0.01655412  0.02858061  0.01641263  0.02631680
  0.00927429  0.01601203  0.00919503  0.01474375
  0.02014417  0.03477882  0.01997199  0.03202406
  0.01595578  0.02754758  0.01581940  0.02536559
  0.01537768  0.02654950  0.01524625  0.02444657
  0.00861521  0.01487412  0.00854157  0.01369597
  0.01871260  0.03230723  0.01855267  0.02974824
  0.01482186  0.02558988  0.01469518  0.02356296



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               0.5024 (0.0294 0.0586)
Shig4337             0.5024 (0.0294 0.0586)-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):  -1022.760102     +0.000000
   4..1     4..5     5..2     5..3  
  0.50096  3.71327  0.00000  0.00000  0.05637  0.96759  0.00000  0.17487 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   4.21425

(1: 0.500963, (2: 0.000004, 3: 0.000004): 3.713275);

(K12: 0.500963, (S2457T: 0.000004, Shig4337: 0.000004): 3.713275);

Detailed output identifying parameters

kappa (ts/tv) =  0.05637


dN/dS for site classes (K=3)

p:   0.96759  0.00000  0.03241
w:   0.17487  1.00000999.00000

dN & dS for each branch

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

   4..1       0.501    115.3    616.7  32.5428   0.1971   0.0061    0.7  121.5
   4..5       3.713    115.3    616.7  32.5428   1.4609   0.0449    5.2  900.9
   5..2       0.000    115.3    616.7  32.5428   0.0000   0.0000    0.0    0.0
   5..3       0.000    115.3    616.7  32.5428   0.0000   0.0000    0.0    0.0


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

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

    67 V      0.694         693.245
   196 R      1.000**       998.716
   237 I      0.833         832.568
   243 L      0.998**       996.698
   244 G      0.826         825.006


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

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

    67 V      0.731         6.099 +- 3.784
   196 R      0.901         7.360 +- 3.016
   243 L      0.946         7.652 +- 2.717



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:   0.431  0.274  0.153  0.077  0.036  0.016  0.007  0.003  0.002  0.001
w2:   0.017  0.025  0.037  0.054  0.074  0.098  0.125  0.156  0.190  0.225

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.001
 0.000 0.000 0.000 0.001 0.002
 0.000 0.000 0.000 0.000 0.000 0.002 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.012
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.011 0.026
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.027 0.050
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.011 0.060 0.083
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.007 0.027 0.120 0.114
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.005 0.018 0.061 0.201 0.125

sum of density on p0-p1 =   1.000000
