
seed used = 141393033

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


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b0235.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 235
# site patterns = 129
    3    3    1    1    2    2    3    5    1    3    3    1    2    2    3
    3    1    1    1    1    1    1    2    1    1    1    1    1    2    1
    1    1    1    1    1    2    2    2    1    1    2    1    4   12    1
    5    2    6    4    1    2    5    1    3    5    1    3    1    1    1
    1    1    2    3    3    5    7    1    2    2    1    1    2    3    2
    1    1    2    4    6    3    1    3    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    2    1    1    1    1    1    1    1
    1    1    2    1    1    2    2    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1

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



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

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

#1: K12            
position  1:    T:0.19048    C:0.25000    A:0.23810    G:0.32143
position  2:    T:0.28571    C:0.25000    A:0.22619    G:0.23810
position  3:    T:0.23810    C:0.32143    A:0.23810    G:0.20238

#2: S2457T         
position  1:    T:0.18222    C:0.28000    A:0.19556    G:0.34222
position  2:    T:0.29778    C:0.23111    A:0.28000    G:0.19111
position  3:    T:0.27556    C:0.25778    A:0.20000    G:0.26667

#3: Shig4337       
position  1:    T:0.18222    C:0.28000    A:0.19556    G:0.34222
position  2:    T:0.29778    C:0.23111    A:0.28000    G:0.19111
position  3:    T:0.27556    C:0.25778    A:0.20000    G:0.26667

#4: CFT073         
position  1:    T:0.17447    C:0.28085    A:0.19574    G:0.34894
position  2:    T:0.30213    C:0.21702    A:0.29787    G:0.18298
position  3:    T:0.28085    C:0.24681    A:0.19149    G:0.28085

#5: O157           
position  1:    T:0.19048    C:0.25000    A:0.25000    G:0.30952
position  2:    T:0.28571    C:0.25000    A:0.22619    G:0.23810
position  3:    T:0.23810    C:0.32143    A:0.23810    G:0.20238

#6: EDL933         
position  1:    T:0.19048    C:0.25000    A:0.25000    G:0.30952
position  2:    T:0.28571    C:0.25000    A:0.22619    G:0.23810
position  3:    T:0.23810    C:0.32143    A:0.23810    G:0.20238

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      29 | Ser S TCT      15 | Tyr Y TAT       7 | Cys C TGT       2
      TTC      15 |       TCC       9 |       TAC      15 |       TGC       1
Leu L TTA      36 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG       9 |       TCG      12 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT       3 | Pro P CCT       3 | His H CAT      22 | Arg R CGT      18
      CTC       6 |       CCC      18 |       CAC      14 |       CGC      27
      CTA       9 |       CCA       8 | Gln Q CAA      30 |       CGA       3
      CTG      46 |       CCG      22 |       CAG      22 |       CGG       4
------------------------------------------------------------------------------
Ile I ATT      25 | Thr T ACT       0 | Asn N AAT      16 | Ser S AGT      12
      ATC      32 |       ACC      15 |       AAC      25 |       AGC       8
      ATA       3 |       ACA       5 | Lys K AAA       7 | Arg R AGA       6
Met M ATG      24 |       ACG       6 |       AAG       9 |       AGG       3
------------------------------------------------------------------------------
Val V GTT      19 | Ala A GCT      19 | Asp D GAT      38 | Gly G GGT      22
      GTC       3 |       GCC       9 |       GAC      17 |       GGC      41
      GTA      12 |       GCA      35 | Glu E GAA      22 |       GGA      13
      GTG       6 |       GCG      36 |       GAG       9 |       GGG      14
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.18250    C:0.27215    A:0.20918    G:0.33618
position  2:    T:0.29562    C:0.23266    A:0.27001    G:0.20171
position  3:    T:0.26681    C:0.27215    A:0.20811    G:0.25293

Codon frequencies under model, for use in evolver:
  0.01484552  0.01514243  0.01157950  0.01407355
  0.01168347  0.01191714  0.00911311  0.01107593
  0.01355926  0.01383045  0.00000000  0.00000000
  0.01012925  0.01033184  0.00000000  0.00960253
  0.02213805  0.02258081  0.01726768  0.02098687
  0.01742272  0.01777118  0.01358973  0.01651674
  0.02021995  0.02062435  0.01577156  0.01916851
  0.01510502  0.01540712  0.01178192  0.01431956
  0.01701591  0.01735623  0.01327241  0.01613108
  0.01339158  0.01365942  0.01044544  0.01269522
  0.01554161  0.01585244  0.01212246  0.01473345
  0.01161014  0.01184234  0.00905591  0.01100641
  0.02734700  0.02789394  0.02133066  0.02592496
  0.02152219  0.02195263  0.01678731  0.02040304
  0.02497759  0.02547714  0.01948252  0.02367875
  0.01865915  0.01903233  0.01455413  0.01768887



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                 
S2457T               0.3705 (0.1073 0.2896)
Shig4337             0.3705 (0.1073 0.2896)-1.0000 (0.0000 0.0000)
CFT073               0.4735 (0.0952 0.2011) 0.1161 (0.0179 0.1539) 0.1161 (0.0179 0.1539)
O157                -1.0000 (0.0053 0.0000) 0.3916 (0.1134 0.2896) 0.3916 (0.1134 0.2896) 0.5034 (0.1012 0.2011)
EDL933              -1.0000 (0.0053 0.0000) 0.3916 (0.1134 0.2896) 0.3916 (0.1134 0.2896) 0.5034 (0.1012 0.2011)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 10  np: 15):  -1247.746964     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.00000  6.17784  0.00000  0.00000  0.00000  3.04748  0.00581  0.00000  0.00000  2.85736  0.94392  0.00000  0.10396 501.03465
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   9.23115

((1: 0.000004, (2: 0.000004, 3: 0.000004): 6.177839): 0.000000, (4: 3.047476, (5: 0.000004, 6: 0.000004): 0.005813): 0.000000);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 6.177839): 0.000000, (CFT073: 3.047476, (O157: 0.000004, EDL933: 0.000004): 0.005813): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.85736


dN/dS for site classes (K=3)

p:   0.94392  0.00000  0.05608
w:   0.10396  1.00000501.03465

dN & dS for each branch

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

   7..8       0.000    212.9    492.1  28.1965   0.0000   0.0000    0.0    0.0
   8..1       0.000    212.9    492.1  28.1965   0.0000   0.0000    0.0    0.0
   8..9       6.178    212.9    492.1  28.1965   2.9058   0.1031   21.9 1429.8
   9..2       0.000    212.9    492.1  28.1965   0.0000   0.0000    0.0    0.0
   9..3       0.000    212.9    492.1  28.1965   0.0000   0.0000    0.0    0.0
   7..10      0.000    212.9    492.1  28.1965   0.0000   0.0000    0.0    0.0
  10..4       3.047    212.9    492.1  28.1965   1.4334   0.0508   10.8  705.3
  10..11      0.006    212.9    492.1  28.1965   0.0027   0.0001    0.0    1.3
  11..5       0.000    212.9    492.1  28.1965   0.0000   0.0000    0.0    0.0
  11..6       0.000    212.9    492.1  28.1965   0.0000   0.0000    0.0    0.0


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

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

    88 A      0.997**       499.666
    89 R      1.000**       500.842
    90 R      1.000**       501.035
    91 R      1.000**       501.026
   134 N      1.000**       501.034
   139 *      0.738         369.680
   169 A      1.000**       501.035
   171 N      1.000**       501.035
   231 N      1.000**       501.035
   232 G      1.000**       500.987
   234 L      1.000**       501.008


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

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

    89 R      0.988*        10.217 +- 1.190
    90 R      1.000**       10.342 +- 0.412
    91 R      0.999**       10.329 +- 0.537
   134 N      0.998**       10.327 +- 0.551
   169 A      0.999**       10.336 +- 0.469
   171 N      1.000**       10.342 +- 0.412
   231 N      1.000**       10.341 +- 0.415
   232 G      0.993**       10.279 +- 0.867
   234 L      0.944         9.818 +- 2.197



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:   0.832  0.160  0.008  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.000  0.000  0.000  0.001  0.014  0.127  0.858

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 0.003 0.006
 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 0.083 0.060
 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 0.027 0.686 0.133

sum of density on p0-p1 =   1.000000
