
seed used = 140030105

K12                                  ATG ATT GAA ATA GAA TCA CGC GAG CTG GCA GAT ATT CCC GTT CTT CAT GCT TAT CCT GTC GGG CAA AAA GAT ACC CCG TTA CCG TGC GTA ATT TTT TAT CAC GGC TTT ACT TCA TCC AGT CTG GTG TAT AGC TAT TTT GCC GTT GCG CTG GCG CAG GCT GGT TTG CGG GTG ATC ATG CCG GAT GCG CCC GAT CAC GGT AGC CGT TTT AGT GGT GAC GCA GCG CGG CGG TTA AAT CAA TTC TGG CAA ATC TTG CTA CAA AGT ATG CAG GAA TTC ACT ACT TTA CGT GCG GCA ATA GCC GAA GAA AAC TGG CTG CTT GAT GAC CGT CTG GCA GTC GGT GGC GCG TCG ATG GGC GCG ATG ACG GCA CTG GGG ATT ACC GCT CGC CAC CCC ACG GTG AGA TGT ACC GCC AGC ATG ATG GGA TCG GGC TAT TTT ACA TCA CTC GCC CGT TCA CTG TTT CCA CCG CTG ATA CCT GAA ACG GCA GCA CAG CAG AAT GAA TTC AAT AAC ATT GTC GCG CCA CTG GCA GAG TGG GAA GCG ACA AAC CAC CTG GAA CAA CTT AGT GAC AGA CCT CTA CTG CTG TGG CAT GGC CTC GAC GAT GAC GTT GTG CCT GCC GAC GAA TCA CTA CGT TTG CAG CAG GCC TTA AGC GAG ACG GGA CGG GAT AAA CTG CTA ACC TGT TCA TGG CAG CCA GGC GTG CGT CAC CGC ATT ACG CCT GAG GCG TTA GAT GCT GCC GTG ACA TTT TTC CGC CAG CAT CTT 
S2457T                               ATG ATT GAA ATA GAA TCA CGC GAG CTG GCA GAT ATT CCC GTT CTT CAT GCT TAT CCT GTC GGG CAA AAA GAT ACC CCG TTA CCG TGC GTA ATT TTT TAT CAC GGC TTT ACT TCA TCC AGC CTG GTG TAT AGC TAT TTT GCC GTT GCG CTG GCG CAG GCT GGT TTG CGG GTG ATC ATG CCG GAT GCG CCC GAT CAC GGT AGC CGT TTT AGT GGC GAC GAA GCG CGG CGG TTA AAT CAA TTC TGG CAA ATC TTG CTA CAA AGT ATG CAG GAA TTC ACT ACT TTA CGT GCG GCA ATA GCC GAA GAA AAC TGG CTG CTT GAT GAC CGT CTG GCA GTC GGT GGC GCG TCG ATG GGC GCG ATG ACG GCA CTG GGA ATT ACC GCT CGC CAC CCC ACG GTG AAA TGT ACC GCC AGC ATG ATG GGA TCG GGC TAT TTT ACA TCG CTC GCC CGT TCA CTG TTT CCA CCG CTG ATA CCT GAA ACG GCA GCA CAG CAG AAT GAA TTC AAT AAA ATT GTC GCG CCG CTG GCA GAG TGG GAA GCG ACA AAC CAC CTG GAA CAA CTT GGG GAC AGA CCT CTA CTG CTG TGG CAT GGC CTC GAC GAT GAC GTT GTG CCT GCC GAC GAA TCA CTA CGT TTG CAG CAG GCC TTA AGC GAG ACG GGA CGG GAT AAA CTG CTA ACC TGT TCA TGG CAG CCA GGC GTG CGT CAC CGC ATT ACG CCT GAG GCG TTA GAT GCT GCC GTG ACA TTT TTC CGC CAG CAT CTT 
Shig4337                             ATG ATT GAA ATA GAA TCA CGC GAG CTG GCA GAT ATT CCC GTT CTT CAT GCT TAT CCT GTC GGG CAA AAA GAT ACC CCG TTA CCG TGC GTA ATT TTT TAT CAC GGC TTT ACT TCA TCC AGC CTG GTG TAT AGC TAT TTT GCC GTT GCG CTG GCG CAG GCT GGT TTG CGG GTG ATC ATG CCG GAT GCG CCC GAT CAC GGT AGC CGT TTT AGT GGC GAC GAA GCG CGG CGG TTA AAT CAA TTC TGG CAA ATC TTG CTA CAA AGT ATG CAG GAA TTC ACT ACT TTA CGT GCG GCA ATA GCC GAA GAA AAC TGG CTG CTT GAT GAC CGT CTG GCA GTC GGT GGC GCG TCG ATG GGC GCG ATG ACG GCA CTG GGA ATT ACC GCT CGC CAC CCC ACG GTG AAA TGT ACC GCC AGC ATG ATG GGA TCG GGC TAT TTT ACA TCG CTC GCC CGT TCA CTG TTT CCA CCG CTG ATA CCT GAA ACG GCA GCA CAG CAG AAT GAA TTC AAT AAA ATT GTC GCG CCG CTG GCA GAG TGG GAA GCG ACA AAC CAC CTG GAA CAA CTT GGG GAC AGA CCT CTA CTG CTG TGG CAT GGC CTC GAC GAT GAC GTT GTG CCT GCC GAC GAA TCA CTA CGT TTG CAG CAG GCC TTA AGC GAG ACG GGA CGG GAT AAA CTG CTA ACC TGT TCA TGG CAG CCA GGC GTG CGT CAC CGC ATT ACG CCT GAG GCG TTA GAT GCT GCC GTG ACA TTT TTC CGC CAG CAT CTT 
CFT073                               ATG ATT GAA ATA GAA TCA CGC GAG CTG GCA GAT ATT CCC GTT CTT CAT GCT TAT CCT GTC GGG CAA AAA GAT ACC CCG TTA CCG TGT GTG ATT TTT TAT CAC GGC TTT ACT TCG TCC AGT CTG GTG TAT AGC TAT TTT GCC GTT GCG CTG GCG CAG GCT GGT TTG CGG GTG ATC ATG CCG GAT GCG CCC GAT CAC GGT AGC CGT TTT AGT GGC GAC GCA GCG CGG CGG TTA AAT CAA TTC TGG CAA ATC TTG CTA CAA AGT ATG CAG GAA TTC ACT ACC TTA CGT GCG GCA ATA GCC GAA GAA AAC TGG CTG CGT GAT GAC CGT CTG GCA GTC GGT GGC GCG TCG ATG GGC GCG ATG ACG GCA CTG GGA ATT ACC GCT CGC CAC CCC ACG ATA AAA TGT ACC GCC AGC ATG ATG GGA TCG GGC TAT TTT ACA TCG CTC GCC CGT TCA CTG TTT CCA CCG CTG ATA CCT GAA ACG GCA GCA CAG CAG AAT GAA TTC AAT AAC ATT GTC GCG CCG CTG GCA GAG TGG GAA GCG ACA AAC CAC CTG GAA CAA CTT GGT GAC AGA CCT CTA CTG CTG TGG CAT GGC CTT GAC GAT GAC GTC GTG CCT GCC GAC GAA TCA CTA CGT TTG CAG CAG GCC TTA AGC GAG ACG GGG CGG GAT AAA CTG CTA ACC TGT TCA TGG CAG CCA GGC GTG CGT CAC CGC ATT ACG CCT GAG GCG TTA GAT GCT GCC GTG ACA TTT TTC CTC CAG CAT CTT 
O157                                 ATG ATT GAA ATA GAA TCA CGC GAG CTG GCA GAT ATT CCC GTT CTT CAT GCT TAT CCT GTC GGA CAA AAA GAT ACC CCG TTA CCG TGC GTG ATT TTT TAT CAC GGC TTT ACT TCG TCC AGT CTG GTG TAT AGC TAT TTT GCC GTT GCG CTG GCG CAG GCT GGT TTG CGG GTG ATC ATG CCG GAT GCG CCC GAT CAC GGT AGC CGT TTT AGT GGT GAC GCA GCG CGG CGG TTA AAT CAA TTC TGG CAA ATC TTG CTA CAA AGT ATG CAG GAA TTC ACT ACT TTA CGT GCG GCA ATA GCC GAA GAA AAG TGG CTG CTT GAT GAC CGT CTG GCA GTC GGT GGT GCG TCG ATG GGC GCG ATG ACG GCA CTG GGG ATT ACC GCT CGC CAC CCC ACG GTG AGA TGT ACC GCC AGC ATG ATG GGA TCG GGC TAT TTT ACA TCA CTC GCC CGT TCA CTG TTT CCA CCG CTG ATA CCT GAA ACG GTA GCA CAG CAG AAT GAA TTC AAT AAC ATT GTC GCG CCA CTG GCA GAG TGG GAA GCG ACA AAC CAC CTG GAA CAA CTT AGT GAC AGA CCT CTA CTG CTG TGG TAT GGC CTC GAC GAT GAC GTT GTG CCT GCC GAC GAA TCA CTA CGT TTG CAG CAG GCC TTA AGC GAG ACG GGA CGG GAT AAA CTG CTA ACC TGT TCA TGG CAG CCA GGC GTG CGT CAC CGC ATT ACG CCT GAG GCG TTA GAT GCT GCC GTG ACA TTT TTC CGC CAG CAT CTT 
EDL933                               ATG ATT GAA ATA GAA TCA CGC GAG CTG GCA GAT ATT CCC GTT CTT CAT GCT TAT CCT GTC GGA CAA AAA GAT ACC CCG TTA CCG TGC GTG ATT TTT TAT CAC GGC TTT ACT TCG TCC AGT CTG GTG TAT AGC TAT TTT GCC GTT GCG CTG GCG CAG GCT GGT TTG CGG GTG ATC ATG CCG GAT GCG CCC GAT CAC GGT AGC CGT TTT AGT GGT GAC GCA GCG CGG CGG TTA AAT CAA TTC TGG CAA ATC TTG CTA CAA AGT ATG CAG GAA TTC ACT ACT TTA CGT GCG GCA ATA GCC GAA GAA AAG TGG CTG CTT GAT GAC CGT CTG GCA GTC GGT GGT GCG TCG ATG GGC GCG ATG ACG GCA CTG GGG ATT ACC GCT CGC CAC CCC ACG GTG AGA TGT ACC GCC AGC ATG ATG GGA TCG GGC TAT TTT ACA TCA CTC GCC CGT TCA CTG TTT CCA CCG CTG ATA CCT GAA ACG GTA GCA CAG CAG AAT GAA TTC AAT AAC ATT GTC GCG CCA CTG GCA GAG TGG GAA GCG ACA AAC CAC CTG GAA CAA CTT AGT GAC AGA CCT CTA CTG CTG TGG TAT GGC CTC GAC GAT GAC GTT GTG CCT GCC GAC GAA TCA CTA CGT TTG CAG CAG GCC TTA AGC GAG ACG GGA CGG GAT AAA CTG CTA ACC TGT TCA TGG CAG CCA GGC GTG CGT CAC CGC ATT ACG CCT GAG GCG TTA GAT GCT GCC GTG ACA TTT TTC CGC CAG CAT CTT 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4190.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 249
# site patterns = 77
    7    6   10    3    4    3    4   13    6    8    3    2    3    2    4
    5    5    3    1    5    2    4    4    5    1    1    7    5    5    2
    1    1    1    5    4    7   10    8    3    3    4    2    6    2    1
    6    1    3    4    5    4    1    1    1    1    2    5    1    1    1
    2    1    3    1    1    2    1    1    1    1    1    1    1    1    1
    1    1

1       
K12                   ATG ATT GAA ATA TCA CGC GAG CTG GCA GAT CCC GTT CTT CAT GCT TAT CCT GTC GGG CAA AAA ACC CCG TTA TGC GTA TTT CAC GGC ACT TCA TCC AGT GTG AGC GCC GCG CAG GGT TTG CGG ATC CGT AGT GGT GAC GCA AAT TTC TGG CTA ACT AAC CTT GGC TCG ACG GGG GTG AGA TGT GGA ACA TCA CTC CCA GCA AAC CCA AAC AGT AGA CAT CTC GTT GGA CGC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..C ... .A. ... ... ... ... ... ... ... ... ... ... ..A ... .A. ... ... ... ..G ... ... ... ..A ..G ... G.G ... ... ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..C ... .A. ... ... ... ... ... ... ... ... ... ... ..A ... .A. ... ... ... ..G ... ... ... ..A ..G ... G.G ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..G ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ..C ... .G. ... ... ... ..A A.A .A. ... ... ... ..G ... ... ... ... ..G ... G.. ... ... ..T ..C ..G .T. 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ..G ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ..T ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... T.. ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ..G ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ..T ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... T.. ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.16466    C:0.29317    A:0.20482    G:0.33735
position  2:    T:0.29317    C:0.27309    A:0.24900    G:0.18474
position  3:    T:0.26908    C:0.22088    A:0.21687    G:0.29317

#2: S2457T         
position  1:    T:0.16466    C:0.29317    A:0.20080    G:0.34137
position  2:    T:0.29317    C:0.26908    A:0.25703    G:0.18072
position  3:    T:0.25703    C:0.22490    A:0.21687    G:0.30120

#3: Shig4337       
position  1:    T:0.16466    C:0.29317    A:0.20080    G:0.34137
position  2:    T:0.29317    C:0.26908    A:0.25703    G:0.18072
position  3:    T:0.25703    C:0.22490    A:0.21687    G:0.30120

#4: CFT073         
position  1:    T:0.16466    C:0.29317    A:0.20482    G:0.33735
position  2:    T:0.29317    C:0.27309    A:0.25301    G:0.18072
position  3:    T:0.26506    C:0.22490    A:0.20482    G:0.30522

#5: O157           
position  1:    T:0.16867    C:0.28916    A:0.20482    G:0.33735
position  2:    T:0.29719    C:0.26908    A:0.24900    G:0.18474
position  3:    T:0.27309    C:0.21285    A:0.21285    G:0.30120

#6: EDL933         
position  1:    T:0.16867    C:0.28916    A:0.20482    G:0.33735
position  2:    T:0.29719    C:0.26908    A:0.24900    G:0.18474
position  3:    T:0.27309    C:0.21285    A:0.21285    G:0.30120

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      42 | Ser S TCT       0 | Tyr Y TAT      32 | Cys C TGT      13
      TTC      24 |       TCC       6 |       TAC       0 |       TGC       5
Leu L TTA      30 |       TCA      30 | *** * TAA       0 | *** * TGA       0
      TTG      18 |       TCG      18 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT      24 | Pro P CCT      30 | His H CAT      16 | Arg R CGT      37
      CTC      12 |       CCC      18 |       CAC      30 |       CGC      23
      CTA      24 |       CCA      15 | Gln Q CAA      30 |       CGA       0
      CTG      78 |       CCG      27 |       CAG      48 |       CGG      24
------------------------------------------------------------------------------
Ile I ATT      36 | Thr T ACT      17 | Asn N AAT      18 | Ser S AGT      19
      ATC      12 |       ACC      25 |       AAC      14 |       AGC      26
      ATA      19 |       ACA      18 | Lys K AAA      17 | Arg R AGA       9
Met M ATG      42 |       ACG      30 |       AAG       2 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      17 | Ala A GCT      24 | Asp D GAT      48 | Gly G GGT      24
      GTC      19 |       GCC      42 |       GAC      36 |       GGC      37
      GTA       5 |       GCA      44 | Glu E GAA      62 |       GGA      16
      GTG      38 |       GCG      60 |       GAG      24 |       GGG      10
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16600    C:0.29183    A:0.20348    G:0.33869
position  2:    T:0.29451    C:0.27041    A:0.25234    G:0.18273
position  3:    T:0.26573    C:0.22021    A:0.21352    G:0.30054

Codon frequencies under model, for use in evolver:
  0.01336537  0.01107609  0.01073943  0.01511600
  0.01227184  0.01016986  0.00986075  0.01387924
  0.01145169  0.00949020  0.00000000  0.00000000
  0.00829261  0.00687221  0.00000000  0.00937879
  0.02349719  0.01947248  0.01888061  0.02657491
  0.02157469  0.01787928  0.01733583  0.02440060
  0.02013282  0.01668438  0.01617725  0.02276986
  0.01457894  0.01208179  0.01171456  0.01648852
  0.01638336  0.01357714  0.01316446  0.01852929
  0.01504290  0.01246629  0.01208737  0.01701326
  0.01403756  0.01163314  0.01127955  0.01587623
  0.01016513  0.00842400  0.00816795  0.01149658
  0.02726967  0.02259880  0.02191190  0.03084152
  0.02503852  0.02074980  0.02011911  0.02831812
  0.02336515  0.01936306  0.01877452  0.02642557
  0.01691959  0.01402153  0.01359534  0.01913576



Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
S2457T               0.2710 (0.0081 0.0299)
Shig4337             0.2710 (0.0081 0.0299)-1.0000 (0.0000 0.0000)
CFT073               0.1551 (0.0099 0.0639) 0.1890 (0.0099 0.0524) 0.1890 (0.0099 0.0524)
O157                 0.2497 (0.0054 0.0216) 0.2588 (0.0135 0.0523) 0.2588 (0.0135 0.0523) 0.2408 (0.0154 0.0638)
EDL933               0.2497 (0.0054 0.0216) 0.2588 (0.0135 0.0523) 0.2588 (0.0135 0.0523) 0.2408 (0.0154 0.0638)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 30
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1194.493033     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00614  0.00000  0.04471  0.00000  0.00000  0.00264  0.07111  0.02143  0.00000  0.00000  8.28896  0.93332  0.00000  0.00000  6.71554
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.14606

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.044715): 0.006141, (4: 0.071110, (5: 0.000004, 6: 0.000004): 0.021435): 0.002642);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.044715): 0.006141, (CFT073: 0.071110, (O157: 0.000004, EDL933: 0.000004): 0.021435): 0.002642);

Detailed output identifying parameters

kappa (ts/tv) =  8.28896


dN/dS for site classes (K=3)

p:   0.93332  0.00000  0.06668
w:   0.00000  1.00000  6.71554

dN & dS for each branch

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

   7..8       0.006    251.9    495.1   0.4478   0.0014   0.0032    0.8    0.7
   8..1       0.000    251.9    495.1   0.4478   0.0000   0.0000    0.0    0.0
   8..9       0.045    251.9    495.1   0.4478   0.0105   0.0235    5.9    5.2
   9..2       0.000    251.9    495.1   0.4478   0.0000   0.0000    0.0    0.0
   9..3       0.000    251.9    495.1   0.4478   0.0000   0.0000    0.0    0.0
   7..10      0.003    251.9    495.1   0.4478   0.0006   0.0014    0.3    0.3
  10..4       0.071    251.9    495.1   0.4478   0.0167   0.0374    9.4    8.3
  10..11      0.021    251.9    495.1   0.4478   0.0050   0.0113    2.8    2.5
  11..5       0.000    251.9    495.1   0.4478   0.0000   0.0000    0.0    0.0
  11..6       0.000    251.9    495.1   0.4478   0.0000   0.0000    0.0    0.0


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

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

    73 A      1.000**       6.716
   102 N      1.000**       6.716
   105 L      1.000**       6.716
   131 V      1.000**       6.716
   132 R      1.000**       6.716
   159 A      1.000**       6.716
   167 N      1.000**       6.716
   185 S      1.000**       6.716
   193 H      1.000**       6.716
   246 R      1.000**       6.716


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

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

   131 V      0.667         5.009 +- 3.663
   132 R      0.878         6.435 +- 3.062
   185 S      0.939         6.795 +- 2.777



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:   0.645  0.269  0.070  0.013  0.002  0.000  0.000  0.000  0.000  0.000
w2:   0.032  0.045  0.064  0.087  0.108  0.125  0.135  0.138  0.136  0.130

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 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.019
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.011 0.083
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.007 0.050 0.237
 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 0.001 0.003 0.007 0.024 0.175 0.373

sum of density on p0-p1 =   1.000000
