
seed used = 140031045

K12                                  ATG AGC AAA ATA TCA GAT TTA AAT TAT TCT CAA CAC ATT ACA TTA GCC GAC AAT TTT AAA CAA AAA AGT GAA GTT TTA AAT ACC TGG CGT GTT GGA ATG AAT GAT TTT GCC CGT ATT GCC GGG GGG CAG GAT AAC AGA AGG AAT ATT CTT TCT CCT GGA GCA TTT TTA GAG TTT TTG GCA AAG ATA TTT ACC CTG GGT TAT GTG GAT TTT AGC AAA CGC TCC AAC GAA GCG GGT AGA AAT ATG ATG GCT CAT ATT AAG TCC TCA TCT TAT TCT AAA GAT ACT AAT GGC AAT GAA AAA ATG AAG TTT TAC ATG AAT AAT CCT GTA GGG GAA CGA GCG GAT TCA CCC AAG GTG ATT ATA GAA ATT TCA CTT TCC ACT ATC ACT ACT ATG GGG ACT CGT CAA GGA CAT ACA GCC ATT ATA TTT CCA CAA CCT GAT GGT TCG ACT AAC CGT TAT GAA GGG AAG TCC TTT GAA AGA AAA GAT GAG AGT TCA TTA CAC CTG ATT ACT AAC AAG GTT CTG GCG TGT TAC CAA AGT GAA GCT AAC AAG AAA ATA GCG CGT CTA TTA AAT AAT AAT CAG GAG TTA AAT AAT CTA CAG AAA TTA AAT AAT CTA CAG AAG TTA AAT AAT CTA CTG AAG TTA AAT AAT ATA CAG GGG TTA AAT AAT CCT CAG GAG TTA AAT AAT CCG CAG AAT TTA AAT GAT TCT CAG GAG TTA AAT AAC TCG CAG GAA TTA AAT AGT CCA CAG GAG TTA AAT GAT CCG CAG GAG TTA AAT AAT TCT CAG GAC TTA AAT AAC TCT AAG GTG AGT TGT ACA GTT TCA GTT GAT TCT ACG ATT ACG GGT TTA TTA AAA GAA CCA TTG AAT AAT GCA TTA TTA GCA ATA AGG AAC GAA CAT CTG CTA TTA ATG CCT CAT GTA TGT GAT GAA TCG ATT TCA TAC TTA CTG GGC GAA AAA GGT ATA CTT GAA GAA ATA GAT AAG CTC TAC GCA TTA AAT GAT CAC GGA ATT GAT AAT GAC AAA GTA GGT AAC AAT GAA ATT AAT GAC ATC AAA GTT AAC CTG TCT CAT ATT CTT ATT GAT TCC TTA GAT GAT GCA AAG GTT AAC CTT ACA CCG GTC ATC GAT TCG ATT CTG GAG ACT TTT TCA AAA TCC CCA TAT ATT AAT GAT GTA AGA ATA CTG GAT TGG TGT TTT AAT AAA AGC ATG CAA TAT TTT GAT GAT ACT AAA AAG ATA AAG CAT GCA TGC TCC GTA ATA AAT CAT ATT AAT CTT CGC AGC GAT CAG TCT AAA ATA GCT GAG ACA TTA TTT TTC AAT CTC GAT AAA GAA CCC TAT AAA AAT AGC CCT GAA TTA CAG GGG TTG ATT TGG AAT AAG TTG GTT GTA TAT GTC AAT GAA TTT AAC TTA AGT AAT CGA GAA AAA ACA AAT TTA ATA CAA AGG CTA TTT GAT AAT GTT GAG TCT ATA TTT AAT GAA GTA CCT GTC AGC ATT TTA GTG AAT GAT ATT TTT ATG AAT GAT TTC TTT ATG AAA AAT CCT GAG ATG ATT AAT TGG TAC TTC CCT CAG TTA CTT AAG AGT TAT GAG GGT GAA AAG ATT TAT TTT GAT AAT TTA AAA TAT GAT TTA AAT GAT AAT GAT AAG GAA TCT AAT AAA GAA ATT TTG AAG AAT CAA CCA GAT AAT GTT ATC AAA GAA AAA CTG AAT AAT GAA TAC AAA CTT AGA TTT AGA ATG ATG CAA ACT ATC TTG CAA TCG AGA GTT AAT GTA TTA CCA TAT ATT AAT GAA CAG CGT TTA AAT AAA CTA AAT CCA CCG GAA AAT TTA CGT ATA GCA ATA GAA CAC TTT GGG TGG AAG AAT AGA CCT ATC ACT GCA 
O157                                 ATG AGC AAA ATA TCA GAT TTG AAT TAT TCT CAA CAC ATT ACA TTA GCC GAC AAT TTT AAA CAA AAA AGT GAA GTT TTA AAT ACC TGG CGT GTT GGA ATG AAT AAT TTT GCC CGT AAT GCC GGG GGG CAG GAT AAC ACA AGA AAT ATC CTT AAT CCT AAG ACA TTT TTG GAG TTT TTG GTA AAA ATA TTT ACC CTG GGT TAT GTG GAT TTT AGC AAA CGC TCC AAC GAA GCG GGA AGA AAT ATG ATG GCT CAT ATT GAG TCC TCA TCT TAT ATC AAA AAT AAT GAT GGC AGT GAG ATA ATG AAG TTT GTT ATG AAT AAT CCT GAA GGG GAA CGA GCG GAT TCA CCC AAG GTG ATT ATA GAA ATT TCA CTT TCC ACT ATT ACT ACT ATG GGG ACT CGT CAA GGA CAT ACA GCC ATT ATA TTT CCA CAA CCT GAT GGT TCG ACT AAC CGT TAT GAA AGA AAG TCC TTT GAA AGA AAA GAT GAG AGT TCA TTA CAC CTG ATT ACT AAC AAG GTT CTG GCG TGT TAC CAA CGC GAA GCT AAC AAG GAA ATA GCT CGT CTA TTA AAT AAT CAT CAG AAG TTA AAT AAT CTA CAG AAG TTA AAT AAT CTA CAG AAG TTA AAT AAT CTA CAG AAG TTA AAT --- --- --- --- --- --- AAT ATA CAG AAG TTA AAT AAT --- --- --- --- --- --- ATA CAG GAG TTA AAT AAT TCG CAG GAG TTA AAT AAT TCG CAG GAG TTA AAT AAT TCG CAG GAG TTA AAT AAC TCG CAG GAC TTA AAA AAT TCG CAG GTG AGT TGT AAA GGT TCA GTT GAT TTT ACG ATT ACG GAT TTA TTA GAA AAA TCA TTG AAT AAT GCA TTA TTA GCA ATA AGG AAC GAA CAT CTG CTA TTA ATG CCT CAT GTA TGT AGT GAA TCG ATT TCA TAC TTA CTG GGC GAA AAT GGT ATA CTT GAA GAA ATA GAT AAG CTC TAC GAA TTA AAT GAT CAC GGA ATT GAT AAT GAC AAA GAA GGT AAC AAT GAA ATT AAT GAC ATC ATG ATT AAC CTG TCT CAT ATT CTT ATT GAA TCC TTA GAT GAT GCA AAG GTT AAT CTT ACA CCG GTC ATC CAT TCG ATG TTG ATG ACT TTT TTA GAA TTG CCA TAT AAT AAT GAT GTA AAA ATA CTG GAG TGG TGT TTT AAT AAA AGC ATG CAA TAT TTT GAT GAT TCT GCA AAG ATA GAG CAT GCA TGC TCC GTA ATA AAT CAT ATT AAT TTT CGT CGC GAT CAG TCT AAA GTA GCT GAG ACA TTA TTT TTC AAT CTC GAT AAA GAA CCC TAT AAA AAT AGC CCT GAA TTA CAG GAG TTG ATT TGG AAA AAG TTG GTT GTA TAT GTC AAT GAT TTT AAC TTA AGC AAT CGA GAA AAA ACA TAT TTA ATA CAA AGA ATA TTT AAT AAT GTT GAG TCA CTA TTT AAT AAA GTA CCT GTC AGT ATT TTA GTT AAT GAT ATT TTT ATG AAT GAT TTT TTT ATG AAA AAC ACT GAG ATG ATT AAT TGG TAC TTC CCT CGG TTA CTT AAG AGC TAT GAG GAT GAA AAG ATT TAT TTT GAT AAG TTA GGG TAT AAT TTT AAT AAT --- --- AAA GAG TCT AAT GAA GAG ATT ATG AAA AAT CAA CCA AAA GAT GTT ATT GAA GAA AAA CTT AAT AAT GAA TTA AAA CTT AGG TTT AGA ATG ATG CAA ACT ATC TTG AAA TCG GAG GTT AAT GTA TCG CCA TTT ATT GAC CAA CAG CGT TTA AAT ACA CTA AAT CCT CCG GAA AAT TTA CGT ATA GCA ATA GAA AAA TTT GGC TGG AAG AAA AAA ACT ATC ACT GCA 
EDL933                               ATG AGC AAA ATA TCA GAT TTG AAT TAT TCT CAA CAC ATT ACA TTA GCC GAC AAT TTT AAA CAA AAA AGT GAA GTT TTA AAT ACC TGG CGT GTT GGA ATG AAT AAT TTT GCC CGT AAT GCC GGG GGG CAG GAT AAC ACA AGA AAT ATC CTT AAT CCT AAG ACA TTT TTG GAG TTT TTG GTA AAA ATA TTT ACC CTG GGT TAT GTG GAT TTT AGC AAA CGC TCC AAC GAA GCG GGA AGA AAT ATG ATG GCT CAT ATT GAG TCC TCA TCT TAT ATC AAA AAT AAT GAT GGC AGT GAG ATA ATG AAG TTT GTT ATG AAT AAT CCT GAA GGG GAA CGA GCG GAT TCA CCC AAG GTG ATT ATA GAA ATT TCA CTT TCC ACT ATT ACT ACT ATG GGG ACT CGT CAA GGA CAT ACA GCC ATT ATA TTT CCA CAA CCT GAT GGT TCG ACT AAC CGT TAT GAA AGA AAG TCC TTT GAA AGA AAA GAT GAG AGT TCA TTA CAC CTG ATT ACT AAC AAG GTT CTG GCG TGT TAC CAA CGC GAA GCT AAC AAG GAA ATA GCT CGT CTA TTA AAT AAT CAT CAG AAG TTA AAT AAT CTA CAG AAG TTA AAT AAT CTA CAG AAG TTA AAT AAT CTA CAG AAG TTA AAT AAT CTA CAG AAG TTA AAT AAT ATA CAG AAG TTA AAT AAT --- --- --- --- --- --- ATA CAG GAG TTA AAT AAT TCG CAG GAG TTA AAT AAT TCG CAG GAG TTA AAT AAT TCG CAG GAG TTA AAT AAC TCG CAG GAC TTA AAA AAT TCG CAG GTG AGT TGT AAA GGT TCA GTT GAT TTT ACG ATT ACG GAT TTA TTA GAA AAA TCA TTG AAT AAT GCA TTA TTA GCA ATA AGG AAC GAA CAT CTG CTA TTA ATG CCT CAT GTA TGT AGT GAA TCG ATT TCA TAC TTA CTG GGC GAA AAT GGT ATA CTT GAA GAA ATA GAT AAG CTC TAC GAA TTA AAT GAT CAC GGA ATT GAT AAT GAC AAA GAA GGT AAC AAT GAA ATT AAT GAC ATC ATG ATT AAC CTG TCT CAT ATT CTT ATT GAA TCC TTA GAT GAT GCA AAG GTT AAT CTT ACA CCG GTC ATC CAT TCG ATG TTG ATG ACT TTT TTA GAA TTG CCA TAT AAT AAT GAT GTA AAA ATA CTG GAG TGG TGT TTT AAT AAA AGC ATG CAA TAT TTT GAT GAT TCT GCA AAG ATA GAG CAT GCA TGC TCC GTA ATA AAT CAT ATT AAT TTT CGT CGC GAT CAG TCT AAA GTA GCT GAG ACA TTA TTT TTC AAT CTC GAT AAA GAA CCC TAT AAA AAT AGC CCT GAA TTA CAG GAG TTG ATT TGG AAA AAG TTG GTT GTA TAT GTC AAT GAT TTT AAC TTA AGC AAT CGA GAA AAA ACA TAT TTA ATA CAA AGA ATA TTT AAT AAT GTT GAG TCA CTA TTT AAT AAA GTA CCT GTC AGT ATT TTA GTT AAT GAT ATT TTT ATG AAT GAT TTT TTT ATG AAA AAC ACT GAG ATG ATT AAT TGG TAC TTC CCT CGG TTA CTT AAG AGC TAT GAG GAT GAA AAG ATT TAT TTT GAT AAG TTA GGG TAT AAT TTT AAT AAT --- --- AAA GAG TCT AAT GAA GAG ATT ATG AAA AAT CAA CCA AAA GAT GTT ATT GAA GAA AAA CTT AAT AAT GAA TTA AAA CTT AGG TTT AGA ATG ATG CAA ACT ATC TTG AAA TCG GAG GTT AAT GTA TCG CCA TTT ATT GAC CAA CAG CGT TTA AAT ACA CTA AAT CCT CCG GAA AAT TTA CGT ATA GCA ATA GAA AAA TTT GGC TGG AAG AAA AAA ACT ATC ACT GCA 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4253.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 604
# site patterns = 166
   14    4   15   14    7   20    2   52   11    5    9    3   20    5   31
    4    4   21    3   21    9    2    5    7    3    6    2    4   13    9
    1    2    1    7    1    7    1    1    9    5    1    3    7    4    3
    1    6    3    1    3    3    7    2    1    1    2    2    1    4    1
   14    1    2    2    2    9    2    4    5    1    4    4    1    5    1
    6    1    2    1    1    2    1    1    1    1    1    1    1    3    1
    2    1    3    1    1    1    2    2    3    1    1    1    1    2    2
    2    1    6    1    6    1    1    2    1    4    1    1    1    2    3
    1    1    1    1    1    1    2    1    1    1    1    1    1    1    1
    2    1    1    2    1    1    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

K12                                  ATG AGC AAA ATA TCA GAT TTA AAT TAT TCT CAA CAC ATT ACA TTA GCC GAC TTT AGT GAA GTT ACC TGG CGT GGA GAT ATT GGG CAG AAC AGA AGG ATT CTT TCT CCT GGA GCA GAG TTG GCA AAG CTG GGT GTG CGC TCC GCG GGT AGA GCT CAT AAG TCT ACT AAT GGC AAT GAA AAA AAG TAC GTA CGA CCC ACT ATC CCA TCG GGG TGT TAC AGT AAA GCG CTA AAT GAG AAA CTG AAT ATA CAG GGG TTA CCT CCG CAG AAT TTA GAT TCT AAC AGT CCA CCG AAT TCT AAT AAG ACA GTT TCT ACG GGT GAA CCA GCA AGG GTA GAT AAA CTC GCA ATC AAA GTT GAT CCG GTC GAT ATT CTG GAG TCA TCC AGA GAT ACT AAA TGC CTT CGC AGC ATA TTC GGG GAA AGT AAT CTA TCT ATA AGC GTG TTC CCT CAG AAT AAA TTA TTG GAT CTG TAC AGA CAA AGA TTA TAT AAT GAA AAA CCA CAC GGG 
O157                                 ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. .A. ... ... ... .C. ..A ..C ... AA. ... AAG A.. ... ... .T. ..A ... ... ... ... ... ... ..A ... ... ... G.. ATC .A. G.. ... .G. ..G .T. ... GTT .A. ... ... ... ..T ... ... A.A ... ... C.C G.. ..T ... C.. A.. ..G .A. --- --- --- --- --- ATA --- --- --- --- --- ATA ..T .A. T.G T.. ..C ..G ..A C.. .A. .G. .T. ... .A. A.. T.. ... ... ... AG. ..T ... .A. ... .TG A.. ..A ... ... C.. ..G T.. AT. .T. .TG .A. ..G T.. GC. ... T.. ..T C.. G.. ... .A. ..T ..C T.. A.. ..A C.. ..T ..T ..T A.. .G. ..G GGG ..T A.. A.A ..T .TA ..G A.. GAG .CG .T. G.C C.. .C. ..T A.A ..C 
EDL933                               ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. .A. ... ... ... .C. ..A ..C ... AA. ... AAG A.. ... ... .T. ..A ... ... ... ... ... ... ..A ... ... ... G.. ATC .A. G.. ... .G. ..G .T. ... GTT .A. ... ... ... ..T ... ... A.A ... ... C.C G.. ..T ... C.. A.. ..G .A. ... C.. ... AA. ... ATA --- --- --- --- --- ATA ..T .A. T.G T.. ..C ..G ..A C.. .A. .G. .T. ... .A. A.. T.. ... ... ... AG. ..T ... .A. ... .TG A.. ..A ... ... C.. ..G T.. AT. .T. .TG .A. ..G T.. GC. ... T.. ..T C.. G.. ... .A. ..T ..C T.. A.. ..A C.. ..T ..T ..T A.. .G. ..G GGG ..T A.. A.A ..T .TA ..G A.. GAG .CG .T. G.C C.. .C. ..T A.A ..C 



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 21 26 26 | Ser TCT 12  6  6 | Tyr TAT 12 12 12 | Cys TGT  4  4  4
    TTC  3  2  2 |     TCC  7  6  6 |     TAC  6  4  4 |     TGC  1  1  1
Leu TTA 37 33 34 |     TCA  8  9  9 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  6  9  9 |     TCG  5 10 10 |     TAG  0  0  0 | Trp TGG  5  5  5
--------------------------------------------------------------------------
Leu CTT  8  8  8 | Pro CCT 10  8  8 | His CAT  7  9  9 | Arg CGT  7  8  8
    CTC  2  2  2 |     CCC  2  2  2 |     CAC  4  3  3 |     CGC  2  3  3
    CTA  7  7  8 |     CCA  7  4  4 | Gln CAA 10 10 10 |     CGA  2  2  2
    CTG 10  7  7 |     CCG  4  2  2 |     CAG 16 15 16 |     CGG  0  1  1
--------------------------------------------------------------------------
Ile ATT 24 23 23 | Thr ACT 11 11 11 | Asn AAT 69 67 69 | Ser AGT  7  6  6
    ATC  6  6  6 |     ACC  2  2  2 |     AAC 12 11 11 |     AGC  6  6  6
    ATA 17 18 18 |     ACA  6  8  8 | Lys AAA 27 29 29 | Arg AGA  8  6  6
Met ATG 14 18 18 |     ACG  2  2  2 |     AAG 20 19 20 |     AGG  3  2  2
--------------------------------------------------------------------------
Val GTT 11 11 11 | Ala GCT  3  4  4 | Asp GAT 33 25 25 | Gly GGT  7  5  5
    GTC  3  3  3 |     GCC  4  4  4 |     GAC  4  5  5 |     GGC  2  3  3
    GTA  8  8  8 |     GCA  9  7  7 | Glu GAA 29 30 30 |     GGA  4  4  4
    GTG  4  3  3 |     GCG  4  3  3 |     GAG 12 18 18 |     GGG  8  5  5
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.21026    C:0.16225    A:0.38742    G:0.24007
position  2:    T:0.29967    C:0.15894    A:0.43212    G:0.10927
position  3:    T:0.40728    C:0.10927    A:0.29636    G:0.18709

#2: O157           
position  1:    T:0.21525    C:0.15424    A:0.39661    G:0.23390
position  2:    T:0.31186    C:0.14915    A:0.43559    G:0.10339
position  3:    T:0.39492    C:0.10678    A:0.29661    G:0.20169

#3: EDL933         
position  1:    T:0.21477    C:0.15604    A:0.39765    G:0.23154
position  2:    T:0.31208    C:0.14765    A:0.43792    G:0.10235
position  3:    T:0.39430    C:0.10570    A:0.29698    G:0.20302

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      73 | Ser S TCT      24 | Tyr Y TAT      36 | Cys C TGT      12
      TTC       7 |       TCC      19 |       TAC      14 |       TGC       3
Leu L TTA     104 |       TCA      26 | *** * TAA       0 | *** * TGA       0
      TTG      24 |       TCG      25 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT      24 | Pro P CCT      26 | His H CAT      25 | Arg R CGT      23
      CTC       6 |       CCC       6 |       CAC      10 |       CGC       8
      CTA      22 |       CCA      15 | Gln Q CAA      30 |       CGA       6
      CTG      24 |       CCG       8 |       CAG      47 |       CGG       2
------------------------------------------------------------------------------
Ile I ATT      70 | Thr T ACT      33 | Asn N AAT     205 | Ser S AGT      19
      ATC      18 |       ACC       6 |       AAC      34 |       AGC      18
      ATA      53 |       ACA      22 | Lys K AAA      85 | Arg R AGA      20
Met M ATG      50 |       ACG       6 |       AAG      59 |       AGG       7
------------------------------------------------------------------------------
Val V GTT      33 | Ala A GCT      11 | Asp D GAT      83 | Gly G GGT      17
      GTC       9 |       GCC      12 |       GAC      14 |       GGC       8
      GTA      24 |       GCA      23 | Glu E GAA      89 |       GGA      12
      GTG      10 |       GCG      10 |       GAG      48 |       GGG      18
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.21341    C:0.15754    A:0.39385    G:0.23520
position  2:    T:0.30782    C:0.15196    A:0.43520    G:0.10503
position  3:    T:0.39888    C:0.10726    A:0.29665    G:0.19721

Codon frequencies under model, for use in evolver:
  0.02765552  0.00743678  0.02056734  0.01367283
  0.01365209  0.00367115  0.01015303  0.00674956
  0.03909919  0.01051407  0.00000000  0.00000000
  0.00943600  0.00253741  0.00000000  0.00466514
  0.02041586  0.00548998  0.01518322  0.01009355
  0.01007825  0.00271012  0.00749517  0.00498266
  0.02886380  0.00776169  0.02146593  0.01427020
  0.00696585  0.00187317  0.00518048  0.00344390
  0.05103964  0.01372495  0.03795806  0.02523389
  0.02519561  0.00677529  0.01873791  0.01245666
  0.07215950  0.01940423  0.05366484  0.03567549
  0.01741462  0.00468292  0.01295121  0.00860975
  0.03047899  0.00819603  0.02266715  0.01506875
  0.01504589  0.00404595  0.01118959  0.00743866
  0.04309099  0.01158749  0.03204666  0.02130409
  0.01039937  0.00279647  0.00773398  0.00514142



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                 
O157                 0.5468 (0.0811 0.1483)
EDL933               0.5628 (0.0826 0.1467)-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):  -2956.830464     +0.000000
   4..1     4..5     5..2     5..3  
  6.01746  0.00000  0.00000  0.00000  3.11834  0.96921  0.00000  0.54104 666.12007
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   6.01747

(1: 6.017462, (2: 0.000004, 3: 0.000004): 0.000000);

(K12: 6.017462, (O157: 0.000004, EDL933: 0.000004): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  3.11834


dN/dS for site classes (K=3)

p:   0.96921  0.00000  0.03079
w:   0.54104  1.00000666.12007

dN & dS for each branch

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

   4..1       6.017    395.8   1416.2  21.0367   2.5327   0.1204   47.6 3586.9
   4..5       0.000    395.8   1416.2  21.0367   0.0000   0.0000    0.0    0.0
   5..2       0.000    395.8   1416.2  21.0367   0.0000   0.0000    0.0    0.0
   5..3       0.000    395.8   1416.2  21.0367   0.0000   0.0000    0.0    0.0


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

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

    51 S      0.751         500.493
    53 G      0.847         564.448
    91 S      0.947         630.745
   103 Y      0.978*        651.629
   176 S      0.740         493.327
   219 P      0.980*        652.985
   231 S      0.977*        651.132
   369 E      0.572         381.285
   374 S      0.740         493.197
   398 K      0.565         376.283
   522 K      0.892         594.524
   553 Y      0.956*        636.882
   567 R      0.815         542.747
   594 H      0.814         542.628


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

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

    51 S      0.792         6.864 +- 3.593
    53 G      0.772         6.712 +- 3.675
    91 S      0.798         6.913 +- 3.573
   103 Y      0.846         7.305 +- 3.338
   215 G      0.745         6.477 +- 3.757
   219 P      0.878         7.569 +- 3.153
   231 S      0.893         7.676 +- 3.051
   301 D      0.510         4.560 +- 3.987
   342 K      0.529         4.736 +- 4.076
   369 E      0.714         6.225 +- 3.846
   374 S      0.747         6.520 +- 3.791
   398 K      0.745         6.481 +- 3.758
   522 K      0.789         6.845 +- 3.612
   542 D      0.565         5.017 +- 4.023
   553 Y      0.846         7.298 +- 3.343
   567 R      0.760         6.612 +- 3.718
   594 H      0.790         6.845 +- 3.604



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:   0.152  0.187  0.224  0.237  0.152  0.042  0.005  0.000  0.000  0.000
w2:   0.002  0.014  0.029  0.043  0.054  0.075  0.112  0.163  0.222  0.286

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.001
 0.000 0.000 0.000 0.000 0.000 0.001 0.015
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.017 0.050
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.089 0.052
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.012 0.134 0.040
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.007 0.019 0.137 0.031
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.004 0.010 0.022 0.134 0.025
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.003 0.004 0.011 0.024 0.128 0.020

sum of density on p0-p1 =   1.000000
