
seed used = 140008497

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2345.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 355
# site patterns = 98
    3    1    1    1    1    1    1    1    1    1    1    1    1    6    6
    4    6    3   20    4    7   18   14   17    2    5    6    5    8    5
    3   19    4   10    9    5    9    3    2   14    6    1    2    2   10
    3    7    6    1    4    6    6    1    1    2    7    1    3    2    3
    2    2    1    4    3    4    1    1    1    1    1    2    1    1    1
    1    1    1    1    1    1    2    1    1    1    1    1    1    1    1
    1    1    2    1    1    1    2    1

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



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 11 11 12 | Ser TCT  6  6  6 | Tyr TAT 10  7  8 | Cys TGT  2  2  2
    TTC  3  4  4 |     TCC  4  4  4 |     TAC  6  7  7 |     TGC  1  0  0
Leu TTA  6  7  7 |     TCA  5  5  4 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  0  0  0 |     TCG  0  0  0 |     TAG  0  0  0 | Trp TGG  2  2  3
--------------------------------------------------------------------------
Leu CTT  4  4  4 | Pro CCT  3  5  5 | His CAT  8  6  6 | Arg CGT  3  3  3
    CTC  7  7  7 |     CCC  0  0  0 |     CAC  2  2  2 |     CGC  1  2  2
    CTA  3  4  3 |     CCA  7  4  3 | Gln CAA  9  8  8 |     CGA  2  2  2
    CTG  1  1  1 |     CCG  0  0  0 |     CAG  3  3  4 |     CGG  0  0  0
--------------------------------------------------------------------------
Ile ATT 17 17 16 | Thr ACT  6  6  6 | Asn AAT 19 23 23 | Ser AGT  4  4  4
    ATC  8  8  8 |     ACC  4  4  3 |     AAC 16 15 14 |     AGC  6  6  6
    ATA 10  9  9 |     ACA  1  1  1 | Lys AAA 21 23 23 | Arg AGA  6  8  8
Met ATG  3  3  3 |     ACG  3  4  5 |     AAG  6  5  5 |     AGG  2  1  1
--------------------------------------------------------------------------
Val GTT  8  8  9 | Ala GCT  5  5  5 | Asp GAT 19 19 19 | Gly GGT 11  9  9
    GTC  2  1  1 |     GCC  2  2  2 |     GAC 13 13 13 |     GGC  2  2  2
    GTA  5  6  6 |     GCA  6  7  7 | Glu GAA 22 22 22 |     GGA  5  5  6
    GTG  1  1  1 |     GCG  3  2  2 |     GAG  5  5  6 |     GGG  2  2  3
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.15909    C:0.15057    A:0.37500    G:0.31534
position  2:    T:0.25284    C:0.15625    A:0.45170    G:0.13920
position  3:    T:0.38636    C:0.21875    A:0.30682    G:0.08807

#2: S2457T         
position  1:    T:0.15625    C:0.14489    A:0.38920    G:0.30966
position  2:    T:0.25852    C:0.15625    A:0.44886    G:0.13636
position  3:    T:0.38352    C:0.21875    A:0.31534    G:0.08239

#3: Shig4337       
position  1:    T:0.16056    C:0.14085    A:0.38028    G:0.31831
position  2:    T:0.25634    C:0.14930    A:0.45070    G:0.14366
position  3:    T:0.38592    C:0.21127    A:0.30704    G:0.09577

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      34 | Ser S TCT      18 | Tyr Y TAT      25 | Cys C TGT       6
      TTC      11 |       TCC      12 |       TAC      20 |       TGC       1
Leu L TTA      20 |       TCA      14 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       0 |       TAG       0 | Trp W TGG       7
------------------------------------------------------------------------------
Leu L CTT      12 | Pro P CCT      13 | His H CAT      20 | Arg R CGT       9
      CTC      21 |       CCC       0 |       CAC       6 |       CGC       5
      CTA      10 |       CCA      14 | Gln Q CAA      25 |       CGA       6
      CTG       3 |       CCG       0 |       CAG      10 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      50 | Thr T ACT      18 | Asn N AAT      65 | Ser S AGT      12
      ATC      24 |       ACC      11 |       AAC      45 |       AGC      18
      ATA      28 |       ACA       3 | Lys K AAA      67 | Arg R AGA      22
Met M ATG       9 |       ACG      12 |       AAG      16 |       AGG       4
------------------------------------------------------------------------------
Val V GTT      25 | Ala A GCT      15 | Asp D GAT      57 | Gly G GGT      29
      GTC       4 |       GCC       6 |       GAC      39 |       GGC       6
      GTA      17 |       GCA      20 | Glu E GAA      66 |       GGA      16
      GTG       3 |       GCG       7 |       GAG      16 |       GGG       7
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.15864    C:0.14542    A:0.38149    G:0.31445
position  2:    T:0.25590    C:0.15392    A:0.45042    G:0.13975
position  3:    T:0.38527    C:0.21624    A:0.30973    G:0.08876

Codon frequencies under model, for use in evolver:
  0.01621351  0.00910023  0.01303439  0.00373547
  0.00975204  0.00547357  0.00783987  0.00224679
  0.02853817  0.01601775  0.00000000  0.00000000
  0.00885461  0.00496987  0.00000000  0.00204003
  0.01486239  0.00834188  0.01194819  0.00342418
  0.00893937  0.00501744  0.00718655  0.00205956
  0.02615999  0.01468294  0.02103058  0.00602706
  0.00811673  0.00455571  0.00652521  0.00187003
  0.03898963  0.02188389  0.03134461  0.00898291
  0.02345133  0.01316263  0.01885303  0.00540300
  0.06862751  0.03851887  0.05517114  0.01581124
  0.02129323  0.01195135  0.01711809  0.00490579
  0.03213750  0.01803796  0.02583603  0.00740423
  0.01932993  0.01084940  0.01553975  0.00445346
  0.05656674  0.03174947  0.04547522  0.01303253
  0.01755110  0.00985099  0.01410971  0.00404364



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               1.0120 (0.0380 0.0375)
Shig4337             0.9415 (0.0563 0.0598) 0.8350 (0.0175 0.0210)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1671.779623     +0.000000
   4..1     4..5     5..2     5..3  
  0.00041  0.30740  0.00000  0.11101  2.89281  0.98298  0.00024  0.92754 157.93558
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.41882

(1: 0.000411, (2: 0.000004, 3: 0.111005): 0.307403);

(K12: 0.000411, (S2457T: 0.000004, Shig4337: 0.111005): 0.307403);

Detailed output identifying parameters

kappa (ts/tv) =  2.89281


dN/dS for site classes (K=3)

p:   0.98298  0.00024  0.01679
w:   0.92754  1.00000157.93558

dN & dS for each branch

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

   4..1       0.000    245.2    819.8   3.5632   0.0002   0.0000    0.0    0.1
   4..5       0.307    245.2    819.8   3.5632   0.1228   0.0345    8.5  100.7
   5..2       0.000    245.2    819.8   3.5632   0.0000   0.0000    0.0    0.0
   5..3       0.111    245.2    819.8   3.5632   0.0443   0.0124    3.1   36.4


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

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

     5 I      0.999**       157.820
     6 S      0.888         140.389
     9 N      0.616         97.675
    13 T      0.998**       157.692
   276 Y      0.791         125.143
   336 A      0.513         81.497


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

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

     5 I      0.972*        8.122 +- 2.315
     6 S      0.873         7.381 +- 3.092
     9 N      0.771         6.571 +- 3.556
    13 T      0.975*        8.149 +- 2.278
   276 Y      0.849         7.197 +- 3.221



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:   0.108  0.115  0.120  0.121  0.118  0.110  0.099  0.085  0.069  0.054
w2:   0.002  0.009  0.023  0.044  0.071  0.100  0.130  0.164  0.204  0.254

Posterior for p0-p1 (see the ternary graph)

 0.020
 0.004 0.034 0.022
 0.000 0.002 0.008 0.046 0.022
 0.000 0.000 0.001 0.004 0.014 0.056 0.019
 0.000 0.000 0.000 0.000 0.001 0.007 0.023 0.060 0.016
 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.012 0.033 0.056 0.013
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.004 0.018 0.041 0.049 0.011
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.006 0.024 0.044 0.043 0.010
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.004 0.009 0.027 0.042 0.038 0.009
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.006 0.011 0.028 0.039 0.034 0.008

sum of density on p0-p1 =   1.000000
