
seed used = 139990917

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0394.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 348
# site patterns = 81
    8    3    2    6    6    3   15    1   12    4    3    6   12   12   18
    5    7    2    3    7    5    5    9    3    5    2   13   15    7    3
    7    2    1    9    6    5    4    2    9    1    3    8    6    4   11
    1    2    1    6    6    1    1    1    1    2    1    2    5    2    4
    4    1    1    1    1    3    1    1    4    4    1    1    1    1    1
    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  3  3  3  3  3 | Ser TCT  0  0  0  0  0 | Tyr TAT  4  4  4  4  4 | Cys TGT  5  5  5  5  5
    TTC  4  4  4  4  4 |     TCC  2  2  1  2  2 |     TAC  5  5  5  5  5 |     TGC  3  3  3  3  3
Leu TTA  6  6  6  6  6 |     TCA  3  2  3  3  3 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  8  8  9  8  8 |     TCG  4  5  5  4  4 |     TAG  0  0  0  0  0 | Trp TGG  5  5  5  5  5
--------------------------------------------------------------------------------------------------
Leu CTT  0  0  0  0  0 | Pro CCT  4  2  3  4  4 | His CAT  4  4  5  4  4 | Arg CGT 10  9  9 10 10
    CTC  3  3  3  3  3 |     CCC  1  2  2  1  1 |     CAC  3  3  2  3  3 |     CGC  6  6  7  6  6
    CTA  1  1  1  1  1 |     CCA  2  3  3  2  2 | Gln CAA  4  4  4  4  4 |     CGA  0  0  0  0  0
    CTG 12 12 11 12 12 |     CCG  7  7  7  8  8 |     CAG  8  8  8  8  8 |     CGG  7  7  8  7  7
--------------------------------------------------------------------------------------------------
Ile ATT 15 15 15 15 15 | Thr ACT  2  2  2  2  2 | Asn AAT 12 12 12 12 12 | Ser AGT  2  3  2  2  2
    ATC  5  5  5  5  5 |     ACC  5  4  5  5  5 |     AAC  3  3  3  3  3 |     AGC  6  6  6  6  6
    ATA  3  3  3  3  3 |     ACA  0  2  1  0  0 | Lys AAA  7  7  8  7  7 | Arg AGA  0  0  0  0  0
Met ATG  7  6  6  6  6 |     ACG 13 14 13 14 14 |     AAG  4  4  3  4  4 |     AGG  1  1  0  1  1
--------------------------------------------------------------------------------------------------
Val GTT  5  5  5  5  5 | Ala GCT  3  2  2  2  2 | Asp GAT 13 14 13 13 13 | Gly GGT  8  9  7  8  8
    GTC  5  6  5  5  5 |     GCC  5  5  6  6  6 |     GAC  5  4  5  5  5 |     GGC 20 19 21 20 20
    GTA  6  6  7  6  6 |     GCA 10 10 11 10 10 | Glu GAA 15 15 15 15 15 |     GGA  6  6  8  6  6
    GTG 10 10  9 10 10 |     GCG 15 14 14 15 15 |     GAG  7  7  7  7  7 |     GGG  6  6  3  5  5
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.14943    C:0.20690    A:0.24425    G:0.39943
position  2:    T:0.26724    C:0.21839    A:0.27011    G:0.24425
position  3:    T:0.25862    C:0.23276    A:0.18103    G:0.32759

#2: Shig4337       
position  1:    T:0.14943    C:0.20402    A:0.25000    G:0.39655
position  2:    T:0.26724    C:0.21839    A:0.27011    G:0.24425
position  3:    T:0.25575    C:0.22989    A:0.18678    G:0.32759

#3: CFT073         
position  1:    T:0.15230    C:0.20977    A:0.24138    G:0.39655
position  2:    T:0.26437    C:0.22414    A:0.27011    G:0.24138
position  3:    T:0.25000    C:0.23851    A:0.20115    G:0.31034

#4: O157           
position  1:    T:0.14943    C:0.20977    A:0.24425    G:0.39655
position  2:    T:0.26437    C:0.22414    A:0.27011    G:0.24138
position  3:    T:0.25575    C:0.23563    A:0.18103    G:0.32759

#5: EDL933         
position  1:    T:0.14943    C:0.20977    A:0.24425    G:0.39655
position  2:    T:0.26437    C:0.22414    A:0.27011    G:0.24138
position  3:    T:0.25575    C:0.23563    A:0.18103    G:0.32759

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      15 | Ser S TCT       0 | Tyr Y TAT      20 | Cys C TGT      25
      TTC      20 |       TCC       9 |       TAC      25 |       TGC      15
Leu L TTA      30 |       TCA      14 | *** * TAA       0 | *** * TGA       0
      TTG      41 |       TCG      22 |       TAG       0 | Trp W TGG      25
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT      17 | His H CAT      21 | Arg R CGT      48
      CTC      15 |       CCC       7 |       CAC      14 |       CGC      31
      CTA       5 |       CCA      12 | Gln Q CAA      20 |       CGA       0
      CTG      59 |       CCG      37 |       CAG      40 |       CGG      36
------------------------------------------------------------------------------
Ile I ATT      75 | Thr T ACT      10 | Asn N AAT      60 | Ser S AGT      11
      ATC      25 |       ACC      24 |       AAC      15 |       AGC      30
      ATA      15 |       ACA       3 | Lys K AAA      36 | Arg R AGA       0
Met M ATG      31 |       ACG      68 |       AAG      19 |       AGG       4
------------------------------------------------------------------------------
Val V GTT      25 | Ala A GCT      11 | Asp D GAT      66 | Gly G GGT      40
      GTC      26 |       GCC      28 |       GAC      24 |       GGC     100
      GTA      31 |       GCA      51 | Glu E GAA      75 |       GGA      32
      GTG      49 |       GCG      73 |       GAG      35 |       GGG      25
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15000    C:0.20805    A:0.24483    G:0.39713
position  2:    T:0.26552    C:0.22184    A:0.27011    G:0.24253
position  3:    T:0.25517    C:0.23448    A:0.18621    G:0.32414

Codon frequencies under model, for use in evolver:
  0.01044977  0.00960249  0.00762551  0.01327403
  0.00873076  0.00802286  0.00637109  0.01109042
  0.01063072  0.00976877  0.00000000  0.00000000
  0.00954502  0.00877110  0.00000000  0.01212476
  0.01449355  0.01331839  0.01057637  0.01841072
  0.01210933  0.01112749  0.00883654  0.01538212
  0.01474452  0.01354902  0.01075951  0.01872952
  0.01323869  0.01216529  0.00966067  0.01681672
  0.01705594  0.01567303  0.01244623  0.02166565
  0.01425020  0.01309478  0.01039880  0.01810161
  0.01735128  0.01594442  0.01266175  0.02204082
  0.01557924  0.01431605  0.01136863  0.01978984
  0.02766586  0.02542268  0.02018860  0.03514312
  0.02311476  0.02124059  0.01686753  0.02936200
  0.02814492  0.02586290  0.02053818  0.03575165
  0.02527055  0.02322158  0.01844067  0.03210042



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                 
Shig4337             0.1646 (0.0051 0.0312)
CFT073               0.0433 (0.0038 0.0889) 0.0800 (0.0064 0.0803)
O157                 1.0067 (0.0038 0.0038) 0.2366 (0.0064 0.0272) 0.0000 (0.0000 0.0844)
EDL933               1.0067 (0.0038 0.0038) 0.2366 (0.0064 0.0272) 0.0000 (0.0000 0.0844)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, (4, 5)));   MP score: 34
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1596.923329     +0.000000
   6..7     7..1     7..2     6..8     8..3     8..9     9..4     9..5  
  0.00000  0.02417  0.10124  0.00000  0.21849  0.00000  0.00000  0.00000  4.56022  0.99709  0.00000  0.06102 443.85599
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.34391

((1: 0.024171, 2: 0.101239): 0.000000, (3: 0.218491, (4: 0.000004, 5: 0.000004): 0.000000): 0.000000);

((K12: 0.024171, Shig4337: 0.101239): 0.000000, (CFT073: 0.218491, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  4.56022


dN/dS for site classes (K=3)

p:   0.99709  0.00000  0.00291
w:   0.06102  1.00000443.85599

dN & dS for each branch

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

   6..7       0.000    312.5    731.5   1.3526   0.0000   0.0000    0.0    0.0
   7..1       0.024    312.5    731.5   1.3526   0.0087   0.0065    2.0    6.4
   7..2       0.101    312.5    731.5   1.3526   0.0366   0.0271    8.5   26.8
   6..8       0.000    312.5    731.5   1.3526   0.0000   0.0000    0.0    0.0
   8..3       0.218    312.5    731.5   1.3526   0.0790   0.0584   18.2   57.8
   8..9       0.000    312.5    731.5   1.3526   0.0000   0.0000    0.0    0.0
   9..4       0.000    312.5    731.5   1.3526   0.0000   0.0000    0.0    0.0
   9..5       0.000    312.5    731.5   1.3526   0.0000   0.0000    0.0    0.0


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

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

   311 G      1.000**       443.856


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

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

   311 G      0.987*        6.046 +- 2.599
   328 R      0.525         3.499 +- 3.455



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:   0.984  0.016  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.044  0.089  0.120  0.130  0.127  0.117  0.107  0.097  0.088  0.080

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 0.000 0.000 0.021
 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 0.001 0.009 0.969

sum of density on p0-p1 =   1.000000
