
seed used = 139994021

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0839.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 341
# site patterns = 89
    9    8    2    4    3    3    4    4    9   11   11   14    7    5    9
    9    2    1    7   10    6    5    7   13   16    5    8   16   13    4
    9    7    1    3    1    3    5    9    4    2    3    1    3    2    3
    4    4    4    1    1    2    1    1    2    1    1    2    1    2    1
    1    2    2    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    2    1    1    1    1    1    1    1    1    1    1    1

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



Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  7  7  7  7  7 | Ser TCT  3  3  3  3  3 | Tyr TAT  4  3  4  3  3 | Cys TGT  1  1  1  1  1
    TTC  9  9  9  9  9 |     TCC  3  6  3  3  3 |     TAC  4  4  4  5  5 |     TGC  0  0  0  0  0
Leu TTA  5  5  5  5  5 |     TCA  3  1  3  3  3 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  5  4  5  5  5 |     TCG  3  3  3  3  3 |     TAG  0  0  0  0  0 | Trp TGG  5  5  5  5  5
--------------------------------------------------------------------------------------------------
Leu CTT  5  4  5  5  5 | Pro CCT  2  4  2  2  2 | His CAT  1  1  1  1  1 | Arg CGT 10  9 11 10 10
    CTC  4  4  4  4  4 |     CCC  1  0  1  1  1 |     CAC  2  2  2  2  2 |     CGC  3  3  2  3  3
    CTA  0  0  0  0  0 |     CCA  2  2  2  2  2 | Gln CAA  2  2  2  2  2 |     CGA  0  0  0  0  0
    CTG 16 16 16 16 16 |     CCG  7  5  7  7  7 |     CAG 11  9 11 11 11 |     CGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Ile ATT  8  8  9  8  8 | Thr ACT  3  6  4  3  3 | Asn AAT  9  9 10  9  9 | Ser AGT  1  2  2  1  1
    ATC  5  6  4  5  5 |     ACC 14 11 12 14 14 |     AAC  6  5  5  6  6 |     AGC  9  8  8  9  9
    ATA  1  0  1  1  1 |     ACA  1  1  2  1  1 | Lys AAA 18 16 17 17 17 | Arg AGA  0  1  0  0  0
Met ATG  9  9  9  9  9 |     ACG  9  8  9  9  9 |     AAG  4  4  5  5  5 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT  6  6  6  6  6 | Ala GCT  3  2  3  2  2 | Asp GAT 16 16 16 16 16 | Gly GGT 14 15 12 13 13
    GTC  2  2  2  2  2 |     GCC  9 10  9 11 11 |     GAC  3  4  3  3  3 |     GGC  7  6  9  7  7
    GTA  2  2  2  2  2 |     GCA 11 12 11 11 11 | Glu GAA  8  7  8  8  8 |     GGA  3  3  3  3  3
    GTG 13 13 13 13 13 |     GCG 16 14 16 15 15 |     GAG  7  7  7  7  7 |     GGG  6  6  6  7  7
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.15249    C:0.19355    A:0.28446    G:0.36950
position  2:    T:0.28446    C:0.26393    A:0.27859    G:0.17302
position  3:    T:0.27273    C:0.23754    A:0.16422    G:0.32551

#2: Shig4337       
position  1:    T:0.15408    C:0.18429    A:0.28399    G:0.37764
position  2:    T:0.28701    C:0.26586    A:0.26888    G:0.17825
position  3:    T:0.29003    C:0.24169    A:0.15710    G:0.31118

#3: CFT073         
position  1:    T:0.15249    C:0.19355    A:0.28446    G:0.36950
position  2:    T:0.28446    C:0.26393    A:0.27859    G:0.17302
position  3:    T:0.28152    C:0.22581    A:0.16422    G:0.32845

#4: O157           
position  1:    T:0.15249    C:0.19355    A:0.28446    G:0.36950
position  2:    T:0.28446    C:0.26393    A:0.27859    G:0.17302
position  3:    T:0.26393    C:0.24633    A:0.16129    G:0.32845

#5: EDL933         
position  1:    T:0.15249    C:0.19355    A:0.28446    G:0.36950
position  2:    T:0.28446    C:0.26393    A:0.27859    G:0.17302
position  3:    T:0.26393    C:0.24633    A:0.16129    G:0.32845

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      35 | Ser S TCT      15 | Tyr Y TAT      17 | Cys C TGT       5
      TTC      45 |       TCC      18 |       TAC      22 |       TGC       0
Leu L TTA      25 |       TCA      13 | *** * TAA       0 | *** * TGA       0
      TTG      24 |       TCG      15 |       TAG       0 | Trp W TGG      25
------------------------------------------------------------------------------
Leu L CTT      24 | Pro P CCT      12 | His H CAT       5 | Arg R CGT      50
      CTC      20 |       CCC       4 |       CAC      10 |       CGC      14
      CTA       0 |       CCA      10 | Gln Q CAA      10 |       CGA       0
      CTG      80 |       CCG      33 |       CAG      53 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      41 | Thr T ACT      19 | Asn N AAT      46 | Ser S AGT       7
      ATC      25 |       ACC      65 |       AAC      28 |       AGC      43
      ATA       4 |       ACA       6 | Lys K AAA      85 | Arg R AGA       1
Met M ATG      45 |       ACG      44 |       AAG      23 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      30 | Ala A GCT      12 | Asp D GAT      80 | Gly G GGT      67
      GTC      10 |       GCC      50 |       GAC      16 |       GGC      36
      GTA      10 |       GCA      56 | Glu E GAA      39 |       GGA      15
      GTG      65 |       GCG      76 |       GAG      35 |       GGG      32
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.15280    C:0.19174    A:0.28437    G:0.37109
position  2:    T:0.28496    C:0.26431    A:0.27670    G:0.17404
position  3:    T:0.27434    C:0.23953    A:0.16165    G:0.32448

Codon frequencies under model, for use in evolver:
  0.01224956  0.01069532  0.00721802  0.01448873
  0.01136191  0.00992029  0.00669498  0.01343882
  0.01189450  0.01038531  0.00000000  0.00000000
  0.00748162  0.00653234  0.00000000  0.00884922
  0.01537107  0.01342076  0.00905736  0.01818084
  0.01425722  0.01244824  0.00840103  0.01686338
  0.01492553  0.01303175  0.00879483  0.01765386
  0.00938813  0.00819695  0.00553193  0.01110424
  0.02279648  0.01990402  0.01343276  0.02696358
  0.02114456  0.01846170  0.01245938  0.02500970
  0.02213571  0.01932709  0.01304341  0.02618203
  0.01392332  0.01215670  0.00820428  0.01646844
  0.02974893  0.02597434  0.01752948  0.03518691
  0.02759321  0.02409214  0.01625923  0.03263713
  0.02888665  0.02522146  0.01702138  0.03416700
  0.01816964  0.01586424  0.01070641  0.02149097



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                 
Shig4337             0.1773 (0.0152 0.0856)
CFT073               0.0000 (0.0000 0.0451) 0.1600 (0.0152 0.0948)
O157                 0.0000 (0.0000 0.0451) 0.2249 (0.0152 0.0675) 0.0000 (0.0000 0.0493)
EDL933               0.0000 (0.0000 0.0451) 0.2249 (0.0152 0.0675) 0.0000 (0.0000 0.0493)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, 2), (3, (4, 5)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1623.168482     +0.000000
   6..7     7..1     7..2     6..8     8..3     8..9     9..4     9..5  
  0.00310  0.01381  0.10025  0.00017  0.01988  0.01771  0.00000  0.00000  1.70991  0.97205  0.00000  0.00000  6.26745
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.15494

((1: 0.013806, 2: 0.100251): 0.003099, (3: 0.019882, (4: 0.000004, 5: 0.000004): 0.017714): 0.000174);

((K12: 0.013806, Shig4337: 0.100251): 0.003099, (CFT073: 0.019882, (O157: 0.000004, EDL933: 0.000004): 0.017714): 0.000174);

Detailed output identifying parameters

kappa (ts/tv) =  1.70991


dN/dS for site classes (K=3)

p:   0.97205  0.00000  0.02795
w:   0.00000  1.00000  6.26745

dN & dS for each branch

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

   6..7       0.003    268.6    754.4   0.1752   0.0005   0.0026    0.7    0.3
   7..1       0.014    268.6    754.4   0.1752   0.0021   0.0117    3.2    1.6
   7..2       0.100    268.6    754.4   0.1752   0.0149   0.0853   22.9   11.3
   6..8       0.000    268.6    754.4   0.1752   0.0000   0.0001    0.0    0.0
   8..3       0.020    268.6    754.4   0.1752   0.0030   0.0169    4.5    2.2
   8..9       0.018    268.6    754.4   0.1752   0.0026   0.0151    4.0    2.0
   9..4       0.000    268.6    754.4   0.1752   0.0000   0.0000    0.0    0.0
   9..5       0.000    268.6    754.4   0.1752   0.0000   0.0000    0.0    0.0


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

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

   308 S      1.000**       6.267
   334 Y      1.000**       6.267
   335 T      1.000**       6.267
   338 E      1.000**       6.267
   339 P      1.000**       6.267
   340 Q      1.000**       6.267
   341 L      1.000**       6.267


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

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

   334 Y      0.957*        6.233 +- 2.625
   335 T      0.704         4.755 +- 3.413
   340 Q      0.729         4.920 +- 3.374
   341 L      0.910         5.991 +- 2.807



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.033  0.066  0.099  0.123  0.133  0.132  0.124  0.111  0.097  0.083

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 0.004
 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 0.000 0.000 0.004 0.991

sum of density on p0-p1 =   1.000000
