
seed used = 140004705

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1976.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 265
# site patterns = 68
    2    8    2    9    5    2    2   11   17    4    4    8    1    6    8
    9    2    2    4    6    2    2    9    1    6    1    4    1    6   13
    1    2    8    7    3    1    1    2    2    2    1    3    2   13    4
    4    4    2    2    3    6    1    5    3    8    1    1    1    2    1
    1    3    1    1    3    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 13 13 13 13 13 13 | Ser TCT  3  3  3  3  3  3 | Tyr TAT  4  4  4  4  4  4 | Cys TGT  2  3  3  3  2  2
    TTC  3  3  3  3  3  3 |     TCC  0  0  0  0  0  0 |     TAC  0  0  0  0  0  0 |     TGC  3  2  2  2  3  3
Leu TTA  7  7  7  7  7  7 |     TCA  4  5  5  4  4  4 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  6  6  6  6  6  6 |     TCG  3  3  3  4  3  3 |     TAG  0  0  0  0  0  0 | Trp TGG  9  9  9  9  9  9
--------------------------------------------------------------------------------------------------------------
Leu CTT  8  8  8  8  8  8 | Pro CCT  7  7  7  7  7  7 | His CAT  8  8  8  8  8  8 | Arg CGT  6  6  6  6  6  6
    CTC  0  0  0  0  0  0 |     CCC  5  5  5  5  5  5 |     CAC  2  2  2  2  2  2 |     CGC  1  1  1  1  1  1
    CTA  3  2  2  2  3  3 |     CCA  2  2  2  2  2  2 | Gln CAA 11 11 11 11 11 11 |     CGA  0  0  0  0  0  0
    CTG  9 10 10 10  9  9 |     CCG  1  0  0  0  1  1 |     CAG  9  9  9  9  9  9 |     CGG  2  2  2  2  2  2
--------------------------------------------------------------------------------------------------------------
Ile ATT  8  8  8  8  8  8 | Thr ACT  2  1  1  1  2  2 | Asn AAT  3  4  4  4  3  3 | Ser AGT  0  1  1  1  1  1
    ATC  4  4  4  4  4  4 |     ACC  1  1  1  1  1  1 |     AAC  6  6  6  6  6  6 |     AGC  7  6  6  6  6  6
    ATA  2  2  2  2  2  2 |     ACA  1  2  2  2  1  1 | Lys AAA  2  3  3  3  2  2 | Arg AGA  2  2  2  2  2  2
Met ATG  2  2  2  2  2  2 |     ACG  3  2  2  2  3  3 |     AAG  3  2  2  2  3  3 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  8  8  8  8  8  8 | Ala GCT  8 10 10 10  9  9 | Asp GAT 14 13 13 13 14 14 | Gly GGT  4  5  5  5  4  4
    GTC  4  4  4  4  4  4 |     GCC  6  6  6  6  6  6 |     GAC  3  3  3  3  3  3 |     GGC  4  3  3  3  4  4
    GTA  2  2  2  2  2  2 |     GCA  5  4  4  4  4  4 | Glu GAA 18 17 17 17 18 18 |     GGA  2  2  2  2  2  2
    GTG  2  2  2  2  2  2 |     GCG  4  4  4  4  4  4 |     GAG  3  4  4  4  3  3 |     GGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.21509    C:0.27925    A:0.17358    G:0.33208
position  2:    T:0.30566    C:0.20755    A:0.32453    G:0.16226
position  3:    T:0.36981    C:0.18491    A:0.23019    G:0.21509

#2: S2457T         
position  1:    T:0.21887    C:0.27547    A:0.17358    G:0.33208
position  2:    T:0.30566    C:0.20755    A:0.32453    G:0.16226
position  3:    T:0.38491    C:0.17358    A:0.23019    G:0.21132

#3: Shig4337       
position  1:    T:0.21887    C:0.27547    A:0.17358    G:0.33208
position  2:    T:0.30566    C:0.20755    A:0.32453    G:0.16226
position  3:    T:0.38491    C:0.17358    A:0.23019    G:0.21132

#4: CFT073         
position  1:    T:0.21887    C:0.27547    A:0.17358    G:0.33208
position  2:    T:0.30566    C:0.20755    A:0.32453    G:0.16226
position  3:    T:0.38491    C:0.17358    A:0.22642    G:0.21509

#5: O157           
position  1:    T:0.21509    C:0.27925    A:0.17358    G:0.33208
position  2:    T:0.30566    C:0.20755    A:0.32453    G:0.16226
position  3:    T:0.37736    C:0.18113    A:0.22642    G:0.21509

#6: EDL933         
position  1:    T:0.21509    C:0.27925    A:0.17358    G:0.33208
position  2:    T:0.30566    C:0.20755    A:0.32453    G:0.16226
position  3:    T:0.37736    C:0.18113    A:0.22642    G:0.21509

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      78 | Ser S TCT      18 | Tyr Y TAT      24 | Cys C TGT      15
      TTC      18 |       TCC       0 |       TAC       0 |       TGC      15
Leu L TTA      42 |       TCA      26 | *** * TAA       0 | *** * TGA       0
      TTG      36 |       TCG      19 |       TAG       0 | Trp W TGG      54
------------------------------------------------------------------------------
Leu L CTT      48 | Pro P CCT      42 | His H CAT      48 | Arg R CGT      36
      CTC       0 |       CCC      30 |       CAC      12 |       CGC       6
      CTA      15 |       CCA      12 | Gln Q CAA      66 |       CGA       0
      CTG      57 |       CCG       3 |       CAG      54 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      48 | Thr T ACT       9 | Asn N AAT      21 | Ser S AGT       5
      ATC      24 |       ACC       6 |       AAC      36 |       AGC      37
      ATA      12 |       ACA       9 | Lys K AAA      15 | Arg R AGA      12
Met M ATG      12 |       ACG      15 |       AAG      15 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      48 | Ala A GCT      56 | Asp D GAT      81 | Gly G GGT      27
      GTC      24 |       GCC      36 |       GAC      18 |       GGC      21
      GTA      12 |       GCA      25 | Glu E GAA     105 |       GGA      12
      GTG      12 |       GCG      24 |       GAG      21 |       GGG       6
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.21698    C:0.27736    A:0.17358    G:0.33208
position  2:    T:0.30566    C:0.20755    A:0.32453    G:0.16226
position  3:    T:0.37987    C:0.17799    A:0.22830    G:0.21384

Codon frequencies under model, for use in evolver:
  0.02622136  0.01228584  0.01575887  0.01476037
  0.01780463  0.00834224  0.01070046  0.01002247
  0.02783997  0.01304422  0.00000000  0.00000000
  0.01391998  0.00652211  0.00000000  0.00783575
  0.03351774  0.01570450  0.02014394  0.01886760
  0.02275896  0.01066355  0.01367798  0.01281134
  0.03558674  0.01667392  0.02138739  0.02003227
  0.01779337  0.00833696  0.01069370  0.01001613
  0.02097709  0.00982867  0.01260709  0.01180830
  0.01424370  0.00667379  0.00856037  0.00801798
  0.02227197  0.01043538  0.01338531  0.01253720
  0.01113599  0.00521769  0.00669265  0.00626860
  0.04013009  0.01880267  0.02411792  0.02258978
  0.02724882  0.01276725  0.01637636  0.01533874
  0.04260725  0.01996333  0.02560668  0.02398421
  0.02130363  0.00998167  0.01280334  0.01199211



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               0.0777 (0.0049 0.0632)
Shig4337             0.0777 (0.0049 0.0632)-1.0000 (0.0000 0.0000)
CFT073               0.0858 (0.0049 0.0572) 0.0000 (0.0000 0.0055) 0.0000 (0.0000 0.0055)
O157                 0.0000 (0.0000 0.0111) 0.0957 (0.0049 0.0513) 0.0957 (0.0049 0.0513) 0.1081 (0.0049 0.0454)
EDL933               0.0000 (0.0000 0.0111) 0.0957 (0.0049 0.0513) 0.0957 (0.0049 0.0513) 0.1081 (0.0049 0.0454)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 25
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1183.193504     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.05625  0.00370  0.00000  0.00000  0.00000  0.00000  0.04632  0.00000  0.00000 36.49025  0.98416  0.00000  0.00000 13.25295
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.10630

((1: 0.056254, (2: 0.000004, 3: 0.000004): 0.003704): 0.000000, (4: 0.000004, (5: 0.000004, 6: 0.000004): 0.046317): 0.000000);

((K12: 0.056254, (S2457T: 0.000004, Shig4337: 0.000004): 0.003704): 0.000000, (CFT073: 0.000004, (O157: 0.000004, EDL933: 0.000004): 0.046317): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) = 36.49025


dN/dS for site classes (K=3)

p:   0.98416  0.00000  0.01584
w:   0.00000  1.00000 13.25295

dN & dS for each branch

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

   7..8       0.000    268.9    526.1   0.2099   0.0000   0.0000    0.0    0.0
   8..1       0.056    268.9    526.1   0.2099   0.0082   0.0393   10.6    4.3
   8..9       0.004    268.9    526.1   0.2099   0.0005   0.0026    0.7    0.3
   9..2       0.000    268.9    526.1   0.2099   0.0000   0.0000    0.0    0.0
   9..3       0.000    268.9    526.1   0.2099   0.0000   0.0000    0.0    0.0
   7..10      0.000    268.9    526.1   0.2099   0.0000   0.0000    0.0    0.0
  10..4       0.000    268.9    526.1   0.2099   0.0000   0.0000    0.0    0.0
  10..11      0.046    268.9    526.1   0.2099   0.0068   0.0324    8.7    3.6
  11..5       0.000    268.9    526.1   0.2099   0.0000   0.0000    0.0    0.0
  11..6       0.000    268.9    526.1   0.2099   0.0000   0.0000    0.0    0.0


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

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

    41 T      1.000**       13.253
    61 D      1.000**       13.253
   169 P      1.000**       13.253


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

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

    41 T      0.900         6.276 +- 2.926
    61 D      0.900         6.278 +- 2.924
   169 P      0.926         6.433 +- 2.818



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:   0.964  0.035  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.030  0.054  0.082  0.105  0.120  0.127  0.128  0.124  0.118  0.111

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 0.004
 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 0.062
 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 0.004 0.042 0.884

sum of density on p0-p1 =   1.000000
