
seed used = 141393129

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b0256.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 383
# site patterns = 82
    1    1    1    1    1    1    1    1    1    1    1    1    1    1   12
    5    6    7    9    6   14    9    5    4   10    5   10    6   16    5
   10   20    2    6    5    5    5    6    9    8   10   10    5    9    3
    4    5    6    8    3    5    4    6    5    2    7    7   10    4    4
    4    4    2    5    1    5    1    3    1    3    1    1    1    2    3
    3    1    2    1    1    1    1

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



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

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

#1: K12            
position  1:    T:0.14360    C:0.26371    A:0.34204    G:0.25065
position  2:    T:0.24282    C:0.22715    A:0.30548    G:0.22454
position  3:    T:0.26893    C:0.18016    A:0.32115    G:0.22977

#2: CFT073         
position  1:    T:0.14883    C:0.26110    A:0.34204    G:0.24804
position  2:    T:0.24282    C:0.22715    A:0.30548    G:0.22454
position  3:    T:0.26632    C:0.18277    A:0.31854    G:0.23238

#3: EDL933         
position  1:    T:0.14660    C:0.26702    A:0.34031    G:0.24607
position  2:    T:0.23560    C:0.21728    A:0.30890    G:0.23822
position  3:    T:0.26440    C:0.19110    A:0.31414    G:0.23037

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      13 | Ser S TCT      17 | Tyr Y TAT      14 | Cys C TGT       3
      TTC      15 |       TCC       3 |       TAC      12 |       TGC       7
Leu L TTA      17 |       TCA      31 | *** * TAA       0 | *** * TGA       0
      TTG      11 |       TCG       6 |       TAG       0 | Trp W TGG      19
------------------------------------------------------------------------------
Leu L CTT      16 | Pro P CCT      15 | His H CAT      26 | Arg R CGT      30
      CTC       7 |       CCC       6 |       CAC      12 |       CGC      19
      CTA      18 |       CCA      14 | Gln Q CAA      16 |       CGA      26
      CTG      50 |       CCG      12 |       CAG      21 |       CGG      15
------------------------------------------------------------------------------
Ile I ATT      18 | Thr T ACT      15 | Asn N AAT      31 | Ser S AGT      13
      ATC      18 |       ACC       9 |       AAC      30 |       AGC      12
      ATA      30 |       ACA      47 | Lys K AAA      63 | Arg R AGA      32
Met M ATG      17 |       ACG      18 |       AAG      21 |       AGG      18
------------------------------------------------------------------------------
Val V GTT      24 | Ala A GCT      27 | Asp D GAT      27 | Gly G GGT      17
      GTC       9 |       GCC      17 |       GAC       9 |       GGC      27
      GTA       9 |       GCA       5 | Glu E GAA      38 |       GGA      19
      GTG       4 |       GCG      15 |       GAG      32 |       GGG       6
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.14634    C:0.26394    A:0.34146    G:0.24826
position  2:    T:0.24042    C:0.22387    A:0.30662    G:0.22909
position  3:    T:0.26655    C:0.18467    A:0.31794    G:0.23084

Codon frequencies under model, for use in evolver:
  0.00972108  0.00673487  0.01159541  0.00841858
  0.00905188  0.00627123  0.01079717  0.00783904
  0.01239790  0.00858940  0.00000000  0.00000000
  0.00926320  0.00641764  0.00000000  0.00802206
  0.01753266  0.01214681  0.02091315  0.01518352
  0.01632571  0.01131062  0.01947347  0.01413827
  0.02236050  0.01549159  0.02667184  0.01936449
  0.01670685  0.01157468  0.01992811  0.01446835
  0.02268252  0.01571469  0.02705595  0.01964336
  0.02112105  0.01463288  0.02519340  0.01829110
  0.02892844  0.02004192  0.03450614  0.02505240
  0.02161414  0.01497450  0.02578158  0.01871813
  0.01649112  0.01142522  0.01967078  0.01428153
  0.01535586  0.01063870  0.01831663  0.01329838
  0.02103215  0.01457130  0.02508737  0.01821412
  0.01571436  0.01088708  0.01874426  0.01360885



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               0.5022 (0.0035 0.0070)
EDL933               0.8653 (0.0309 0.0357) 0.8999 (0.0321 0.0357)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1732.546585     +0.000000
   4..1     4..5     5..2     5..3  
  0.00692  0.00000  0.00669  0.53046  4.81307  0.95387  0.00000  0.00000 562.65946
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.54408

(1: 0.006923, (2: 0.006694, 3: 0.530462): 0.000000);

(K12: 0.006923, (CFT073: 0.006694, EDL933: 0.530462): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  4.81307


dN/dS for site classes (K=3)

p:   0.95387  0.00000  0.04613
w:   0.00000  1.00000562.65946

dN & dS for each branch

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

   4..1       0.007    333.5    815.5  25.9576   0.0032   0.0001    0.0    2.6
   4..5       0.000    333.5    815.5  25.9576   0.0000   0.0000    0.0    0.0
   5..2       0.007    333.5    815.5  25.9576   0.0031   0.0001    0.0    2.5
   5..3       0.530    333.5    815.5  25.9576   0.2453   0.0094    3.2  200.0


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

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

     1 M      1.000**       562.659
     2 R      0.997**       561.129
     3 R      1.000**       562.659
     4 T      1.000**       562.659
     5 F      1.000**       562.659
     6 T      1.000**       562.659
     7 A      1.000**       562.659
     8 E      1.000**       562.659
     9 E      1.000**       562.659
    10 K      1.000**       562.659
    11 A      1.000**       562.659
    12 S      1.000**       562.659
    13 V      1.000**       562.659
    14 F      1.000**       562.658
   145 P      1.000**       562.659
   197 H      1.000**       562.659
   261 V      1.000**       562.659


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

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

     1 M      0.997**       10.158 +- 0.798
     2 R      0.939         9.602 +- 2.374
     3 R      0.997**       10.160 +- 0.788
     4 T      0.972*        9.929 +- 1.646
     5 F      0.846         8.738 +- 3.440
     6 T      0.995**       10.138 +- 0.909
     7 A      0.984*        10.042 +- 1.303
     8 E      0.986*        10.053 +- 1.263
     9 E      0.986*        10.061 +- 1.233
    10 K      0.998**       10.167 +- 0.747
    11 A      0.986*        10.061 +- 1.235
    12 S      0.990*        10.094 +- 1.108
    13 V      0.846         8.740 +- 3.438
    14 F      0.847         8.752 +- 3.426
   145 P      0.848         8.761 +- 3.418
   197 H      0.847         8.749 +- 3.429
   261 V      0.847         8.750 +- 3.428



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:   0.249  0.188  0.143  0.110  0.085  0.067  0.053  0.042  0.034  0.028
w2:   0.000  0.000  0.000  0.000  0.000  0.001  0.008  0.044  0.194  0.752

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.002 0.000 0.000
 0.011 0.007 0.003 0.000 0.000
 0.004 0.011 0.015 0.009 0.004 0.000 0.000
 0.001 0.003 0.006 0.015 0.020 0.011 0.004 0.000 0.000
 0.000 0.000 0.001 0.004 0.008 0.020 0.028 0.014 0.006 0.000 0.000
 0.000 0.000 0.000 0.000 0.001 0.005 0.012 0.029 0.039 0.019 0.007 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.007 0.018 0.041 0.054 0.024 0.009 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.011 0.026 0.059 0.076 0.032 0.010 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 0.017 0.040 0.086 0.108 0.041 0.013 0.000 0.000

sum of density on p0-p1 =   1.000000
