
seed used = 139989561

K12                                  ATG AAC TCA ATT TTT ACC GAA GAG AAT CTG TTG GCA TTT ACT ACC GCT GCG CGT TTT GGC AGC TTC AGT AAA GCC GCA GAA GAG TTG GGT TTA ACC ACT TCC GCC ATT AGC TAC ACC ATT AAG CGT ATG GAG ACG GGG CTG GAT GTG GTG CTG TTC ACT CGC AGT ACC CGC AGC ATT GAG TTA ACG GAG TCC GGG CGT TAT TTT TTC CGC AAA GCT ACC GAC CTG CTG AAT GAT TTT TAT GCC ATC AAA CGC AGA ATC GAT ACT ATT TCG CAG GGC ATA GAA GCG CGT GTG CGC ATT TGT ATT AAT CAG CTG CTT TAT ACG CCC AAA CAC ACC GCA CGC TTG TTA CAG GTG CTG AAA AAG CAG TTT CCT ACC TGC CAG ATT ACC GTC ACC ACC GAA GTG TAT AAC GGC GTC TGG GAT GCG ATT ATT AAT AAT CAG GCC AAT ATC GCC ATC GGC GCA CCC GAT ACA CTA CTG GAC GGC GGC GGT ATT GAT TAC ACT GAA ATT GGC GCG ATT CGC TGG GCT TTT GCT ATC GCC CCG GAT CAC CCG TTA GCC TTT GTG CCG GAA CCC ATC GCC GAA AGC CAA CTG CGT CTC TAC CCT AAT ATT ATG GTG GAG GAC ACC GCG CAT ACG ATT AAT AAA AAA GTG GGC TGG TTG CTG CAC GGG CAG GAG TCA ATT CTG GTG CCA GAT TTC AAC ACC AAA TGT CAG TGC CAG ATT TTA GGT GAA GGA ATT GGT TTT TTG CCG GAT TAC ATG GTC CGT GAG GCG ATG ACG CAA TCC CTG CTG GTT ACC CGA CAA ATC CAT AAT CCG CGC CAG GAT TCG CGC ATG TTA CTG GCG ACT CAG CAT TCT GCT ACG GGT CAG GTG ACG CAG TGG ATT AAA AAA CAA TTT GCG CCA AAT GGC ATA TTA ACG GGG ATC TAT 
CFT073                               ATG AAC TCA ATT TTT ACC GAA GAG AAT CTG TTG GCA TTT ACT ACC GCT GCG CGT TTT GGC AGC TTC AGT AAA GCC GCA GAA GAG TTG GGT TTA ACC ACT TCC GCC ATT AGC TAC ACC ATT AAA CGT ATG GAG ACG GGG CTG GAT GTG GTG CTG TTC ACT CGC AGT ACC CGC AGC ATT GAG TTA ACG GAG TCC GGG CGT TAT TTT TTC CGC AAA GCT ACC GAC CTG CTG AAT GAT TTT CAT GCC ATT AAA CGC AGT ATC GAT ACT ATT TCG CAG GGC ATA GAA GCG CGT GTG CGC ATT TGT ATT AAT CAG CTG CTT TAT ACG CCC AAA CAC ACC GCA CGC TTA TTA CAG GTG CTG AAA AAG CAG TTT CCT ACC TGC CAG ATT ACC GTC ACC ACC GAA GTG TAT AAC GGC GTC TGG GAT GCG ATT ATT AAT AAT CAG GCA AAT ATC GCT ATC GGC GCC CCC GAC ACG CTG CTG GAC GGT GGC GGC ATT GAT TAC ACG GAG ATT GGC GCG ATT CGC TGG GCT TTT GCC ATC GCC CCG GAT CAC CCA TTA GCC TTT GTG CCG GAG CCG ATC GCC GAA AGC CAG CTG CGT CTC TAC CCT AAT ATC ATG GTG GAG GAC ACC GCG CAT ACG ATT AAT AAA AAA GTG GGC TGG TTG CTG CAT GGG CAG GAG TCA ATT CTG GTG CCA GAT TTC AAC ACC AAA TGT CAG TGC CAG ATT TTA GGT GAA GGA ATT GGT TTT TTG CCG GAT TAC ATG GTC CGT GAG GCG ATG GCG CAA TCC TTG CTG GTT ACC CGA CAA ATC CAT AAC CCG CGC CAG GAT TCA CGC ATG TTA CTC GCA ACC CAG CAC TCT GCC ACC GGT CAG GTG ACG CAG TGG ATT AAA AAA CAA TTT GCG CCA AAT GGC ATA TTA ACG GGG ATC TAT 
EDL933                               ATG AAC TCA ATT TTT ACC GAA GAG AAT CTG TTG GCA TTT ACT ACC GCT GCG CGT TTT GGC AGT TTC AGT AAA GCC GCA GAA GAG TTG GGT TTA ACC ACT TCC GCC ATT AGC TAC ACC ATC AAG CGA ATG GAA ACA GGG CTG GAT GTG GTG CTG TTC ACT CGC AGT ACC CGC AGC ATT GAG TTA ACG GAG TCC GGG CGT TAT TTT TTC CGC AAA GCT ACC GAC CTG CTG AAT GAT TTT CAC GCC ATC AAA CGC AGC ATC GAT ACT ATT TCG CAG GGC ATA GAA GCG CGT GTG CGC ATT TGT ATT AAT CAG TTG CTT TAT ACG CCC AAA CAC ACC GCA CGC TTA TTA CAG GTG CTG AAA AAG CAG TTT CCT ACC TGC CAG ATT ACC GTC ACC ACC GAA GTG TAT AAC GGC GTC TGG GAT GCG ATT ATT AAT AAT CAG GCA AAT ATC GCT ATC GGC GCA CCC GAC ACG CTG CTG GAC GGC GGC GGT ATT GAT TAC ACT GAA ATT GGC GCG ATT CGC TGG GCT TTT GCT ATC GCC CCG GAT CAC CCG TTA GCC TTT GTG CCG GAA CCA TCG CCG AAA --- --- --- --- --- --- --- --- --- --- --- --- --- --- GCC AAC TGC GTC TCT ACC CTA ATA TTA TGG TGG AGG ACA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- CCG CGC --- --- ATA CGA TTA ATA AAA AAG TGG GCT GGT TGC TGC ACG GGC AGG AGT CAA TTC TGG TGC CAG ATT TCA --- ACA CCA AAT --- --- GTC AGT GCC AGA TTT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0316.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 302
# site patterns = 159
    2    2    1   12    8   11    4    4    7    7    2    3    4    3    4
    3    6    1    3    2    5    5    1    4    2    2    2    1    1    1
    1    1    2    6    6    8    2    3    2    1    1    1    4    1    6
    1    1    1    1    2    2    1    1    1    1    2    4    1    1    1
    1    1    1    1    1    1    2    1    3    1    1    1    1    1    1
    1    3    2    1    2    1    1    1    3    2    3    1    3    1    1
    1    1    1    1    1    1    1    1    1    1    1    4    1    3    1
    3    1    1    1    1    1    1    2    1    1    2    1    1    1    1
    1    2    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1

K12                                  ATG AAC TCA ATT TTT ACC GAA GAG AAT CTG TTG GCA ACT GCT GCG CGT GGC AGC TTC AGT AAA GCC GGT TTA TCC AGC TAC ATT AAG CGT GAG ACG GGG GAT GTG CGC ACG TAT GAC TAT ATC AGA ATC TCG CAG ATA TGT CTG CTT CCC CAC TTG AAG CCT TGC GTC TGG GCC GCC GCA GAT ACA CTA GGC GGT ACT GAA GCT CCG CCG CCC ATC GCC GAA AGC CAA CTG CGT CTC TAC CCT AAT ATT ATG GTG GAG GAC ACC GCG CAT ACG ATT AAT AAA AAA GTG GGC TTG CTG CAC GGG CAG TCA ATT CCA GAT TTC AAC AAA TGT TGC TTA GGT GAA GGA TTT TTG CCG GTC GCG ACG CAA TCC CTG GTT CGA ATC CAT AAT TCG CGC ATG TTA CTG GCG ACT CAG CAT TCT GCT ACG GGT CAG GTG ACG CAG ATT AAA AAA CAA GCG CCA GGC ATA TTA ACG GGG ATC TAT 
CFT073                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... C.. ..T ..T ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ..A ..T ..C ..C ..G ..G ..T ..C ..G ..G ..C ... ..A ..G ... ... ... ... ..G ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... T.. ... ... ... ... ..C ..A ... ... ... ..C ..A ..C ... ..C ... ..C ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ..C ... ..A ..A ..A ... ... ... ... ... ... ... C.C ... ..C ... ... ... ... ... T.. ... ... ... ..A ... ... ... ... ... ..A ..T ... ..C ..G ..G ... ... ... ... ... ... ... ..A TCG C.G A.. --- --- --- --- --- --- --- --- --- --- --- --- --- --- ..C A.C TGC G.C TC. .CC CT. A.A TTA .G. AG. ACA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATA ..A T.A A.. AAA AA. TGG GCT GG. .GC TGC ... ..C AG. AGT CAA TTC TGC C.G .TT TC. A.A ... --- --- G.C .GT .CC .GA .T. 



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

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

#1: K12            
position  1:    T:0.16887    C:0.22517    A:0.31788    G:0.28808
position  2:    T:0.30464    C:0.24503    A:0.28477    G:0.16556
position  3:    T:0.29139    C:0.26821    A:0.14570    G:0.29470

#2: CFT073         
position  1:    T:0.16887    C:0.22517    A:0.31457    G:0.29139
position  2:    T:0.30464    C:0.24503    A:0.28477    G:0.16556
position  3:    T:0.27815    C:0.28477    A:0.14238    G:0.29470

#3: EDL933         
position  1:    T:0.19915    C:0.18644    A:0.33898    G:0.27542
position  2:    T:0.28814    C:0.26695    A:0.23729    G:0.20763
position  3:    T:0.27119    C:0.30508    A:0.17797    G:0.24576

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      29 | Ser S TCT       3 | Tyr Y TAT      12 | Cys C TGT       5
      TTC      12 |       TCC       8 |       TAC      10 |       TGC       9
Leu L TTA      22 |       TCA       7 | *** * TAA       0 | *** * TGA       0
      TTG      13 |       TCG       5 |       TAG       0 | Trp W TGG      14
------------------------------------------------------------------------------
Leu L CTT       3 | Pro P CCT       5 | His H CAT       7 | Arg R CGT      15
      CTC       3 |       CCC       7 |       CAC       9 |       CGC      26
      CTA       2 |       CCA       7 | Gln Q CAA       8 |       CGA       4
      CTG      35 |       CCG      15 |       CAG      34 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      51 | Thr T ACT      15 | Asn N AAT      26 | Ser S AGT      10
      ATC      22 |       ACC      42 |       AAC      10 |       AGC      11
      ATA       8 |       ACA       4 | Lys K AAA      28 | Arg R AGA       2
Met M ATG      14 |       ACG      20 |       AAG       6 |       AGG       2
------------------------------------------------------------------------------
Val V GTT       2 | Ala A GCT      15 | Asp D GAT      25 | Gly G GGT      13
      GTC      10 |       GCC      24 |       GAC      10 |       GGC      26
      GTA       0 |       GCA      14 | Glu E GAA      21 |       GGA       2
      GTG      26 |       GCG      20 |       GAG      22 |       GGG      10
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.17738    C:0.21429    A:0.32262    G:0.28571
position  2:    T:0.30000    C:0.25119    A:0.27143    G:0.17738
position  3:    T:0.28095    C:0.28452    A:0.15357    G:0.28095

Codon frequencies under model, for use in evolver:
  0.01534588  0.01554095  0.00838821  0.01534588
  0.01284913  0.01301246  0.00702346  0.01284913
  0.01388437  0.01406086  0.00000000  0.00000000
  0.00907355  0.00918890  0.00000000  0.00907355
  0.01853864  0.01877430  0.01013341  0.01853864
  0.01552244  0.01571976  0.00848472  0.01552244
  0.01677306  0.01698628  0.00916832  0.01677306
  0.01096134  0.01110068  0.00599158  0.01096134
  0.02791096  0.02826576  0.01525641  0.02791096
  0.02336989  0.02366696  0.01277422  0.02336989
  0.02525277  0.02557378  0.01380342  0.02525277
  0.01650291  0.01671269  0.00902066  0.01650291
  0.02471819  0.02503241  0.01351122  0.02471819
  0.02069658  0.02095967  0.01131296  0.02069658
  0.02236408  0.02264837  0.01222443  0.02236408
  0.01461512  0.01480091  0.00798877  0.01461512



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                 
CFT073               0.0298 (0.0044 0.1467)
EDL933               0.5395 (0.1367 0.2535) 0.4335 (0.1322 0.3049)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1740.793650     +0.000000
   4..1     4..5     5..2     5..3  
  0.00306  0.03837  0.07769  0.67999  1.61291  0.82401  0.00000  0.00000  4.07509
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.79911

(1: 0.003059, (2: 0.077687, 3: 0.679987): 0.038374);

(K12: 0.003059, (CFT073: 0.077687, EDL933: 0.679987): 0.038374);

Detailed output identifying parameters

kappa (ts/tv) =  1.61291


dN/dS for site classes (K=3)

p:   0.82401  0.00000  0.17599
w:   0.00000  1.00000  4.07509

dN & dS for each branch

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

   4..1       0.003    226.7    679.3   0.7172   0.0009   0.0013    0.3    0.6
   4..5       0.038    226.7    679.3   0.7172   0.0116   0.0162    3.7    7.9
   5..2       0.078    226.7    679.3   0.7172   0.0236   0.0329    7.5   16.0
   5..3       0.680    226.7    679.3   0.7172   0.2063   0.2877   65.2  140.1


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

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

    80 Y      1.000**       4.075
    85 R      1.000**       4.075
   189 I      1.000**       4.075
   190 A      1.000**       4.075
   191 E      1.000**       4.075
   207 H      1.000**       4.075
   208 T      1.000**       4.075
   209 I      1.000**       4.075
   210 N      1.000**       4.075
   211 K      1.000**       4.075
   212 K      1.000**       4.075
   213 V      1.000**       4.075
   214 G      1.000**       4.075
   216 L      1.000**       4.075
   217 L      1.000**       4.075
   218 H      1.000**       4.075
   254 T      1.000**       4.075
   270 S      1.000**       4.075
   272 M      1.000**       4.075
   273 L      1.000**       4.075
   274 L      1.000**       4.075
   275 A      1.000**       4.075
   276 T      1.000**       4.075
   277 Q      1.000**       4.075
   278 H      1.000**       4.075
   279 S      1.000**       4.075
   280 A      1.000**       4.075
   283 Q      1.000**       4.075
   284 V      1.000**       4.075
   285 T      1.000**       4.075
   286 Q      1.000**       4.075
   288 I      1.000**       4.075
   289 K      1.000**       4.075
   290 K      1.000**       4.075
   291 Q      1.000**       4.075
   293 A      1.000**       4.075
   298 L      1.000**       4.075
   299 T      1.000**       4.075
   300 G      1.000**       4.075
   301 I      1.000**       4.075
   302 Y      1.000**       4.075


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

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

    80 Y      0.675         3.505 +- 2.326
    85 R      0.764         3.932 +- 2.103
   189 I      0.960*        4.843 +- 1.275
   190 A      0.566         2.986 +- 2.419
   207 H      0.535         2.823 +- 2.424
   208 T      0.975*        4.908 +- 1.188
   210 N      0.920         4.674 +- 1.471
   211 K      0.826         4.229 +- 1.906
   212 K      0.945         4.780 +- 1.358
   213 V      0.734         3.800 +- 2.129
   214 G      0.981*        4.930 +- 1.153
   216 L      0.518         2.732 +- 2.380
   217 L      0.894         4.544 +- 1.648
   218 H      0.975*        4.908 +- 1.190
   254 T      0.836         4.274 +- 1.925
   270 S      0.962*        4.854 +- 1.264
   272 M      0.712         3.677 +- 2.202
   273 L      0.591         3.091 +- 2.372
   274 L      0.969*        4.882 +- 1.227
   275 A      0.905         4.611 +- 1.536
   276 T      0.974*        4.906 +- 1.191
   277 Q      0.972*        4.896 +- 1.203
   278 H      0.924         4.696 +- 1.456
   279 S      0.590         3.090 +- 2.387
   280 A      0.944         4.778 +- 1.360
   283 Q      0.839         4.292 +- 1.856
   284 V      0.962*        4.853 +- 1.263
   285 T      0.957*        4.833 +- 1.297
   286 Q      0.975*        4.907 +- 1.188
   288 I      0.944         4.777 +- 1.365
   289 K      0.626         3.260 +- 2.378
   290 K      0.818         4.191 +- 1.934
   291 Q      0.963*        4.858 +- 1.262
   293 A      0.523         2.769 +- 2.412
   298 L      0.848         4.328 +- 1.852
   299 T      0.760         3.909 +- 2.119
   300 G      0.634         3.309 +- 2.371
   301 I      0.797         4.085 +- 2.006



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.004  0.135  0.402  0.310  0.113  0.028  0.006  0.001  0.000

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 0.000 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 0.019 0.006 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 0.005 0.100 0.859 0.011 0.000

sum of density on p0-p1 =   1.000000
