
seed used = 139994153

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0851.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 240
# site patterns = 91
    3    1    1    1    1    1    1    1    1    1    1    1    1   10    1
    1    2    1    1    1    1    1    1    1   13    8    1    2    3    6
    2    4    5    3    3    4    4    1    7    4    3    6    1    5    8
   13    1    7    3    5    2    2    1    4    3    2    4    4    7    8
    1    1    1    1    2    2    1    2    3    6    1    1    1    5    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1

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



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

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

#1: K12            
position  1:    T:0.15833    C:0.28750    A:0.25000    G:0.30417
position  2:    T:0.28333    C:0.22083    A:0.29167    G:0.20417
position  3:    T:0.27083    C:0.25417    A:0.16250    G:0.31250

#2: S2457T         
position  1:    T:0.16667    C:0.27917    A:0.25000    G:0.30417
position  2:    T:0.27917    C:0.22500    A:0.29583    G:0.20000
position  3:    T:0.26667    C:0.25417    A:0.16667    G:0.31250

#3: Shig4337       
position  1:    T:0.17447    C:0.25957    A:0.27234    G:0.29362
position  2:    T:0.30638    C:0.20000    A:0.28936    G:0.20426
position  3:    T:0.25106    C:0.25106    A:0.17021    G:0.32766

#4: CFT073         
position  1:    T:0.15833    C:0.28750    A:0.24583    G:0.30833
position  2:    T:0.28333    C:0.22083    A:0.29583    G:0.20000
position  3:    T:0.27083    C:0.25000    A:0.16667    G:0.31250

#5: O157           
position  1:    T:0.16250    C:0.28750    A:0.25000    G:0.30000
position  2:    T:0.27500    C:0.22917    A:0.29583    G:0.20000
position  3:    T:0.27500    C:0.25000    A:0.16250    G:0.31250

#6: EDL933         
position  1:    T:0.16250    C:0.28750    A:0.25000    G:0.30000
position  2:    T:0.27500    C:0.22917    A:0.29583    G:0.20000
position  3:    T:0.27500    C:0.25000    A:0.16250    G:0.31250

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      25 | Ser S TCT       0 | Tyr Y TAT      30 | Cys C TGT      22
      TTC      17 |       TCC      30 |       TAC       7 |       TGC      10
Leu L TTA      31 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG      31 |       TCG       6 |       TAG       0 | Trp W TGG      26
------------------------------------------------------------------------------
Leu L CTT      19 | Pro P CCT       6 | His H CAT      34 | Arg R CGT      28
      CTC      18 |       CCC       5 |       CAC      12 |       CGC      52
      CTA       0 |       CCA      11 | Gln Q CAA      30 |       CGA       6
      CTG      89 |       CCG      42 |       CAG      48 |       CGG       4
------------------------------------------------------------------------------
Ile I ATT      74 | Thr T ACT       7 | Asn N AAT      36 | Ser S AGT      19
      ATC      28 |       ACC      34 |       AAC      19 |       AGC      36
      ATA       1 |       ACA       6 | Lys K AAA      42 | Arg R AGA       0
Met M ATG      19 |       ACG      35 |       AAG       6 |       AGG       1
------------------------------------------------------------------------------
Val V GTT      12 | Ala A GCT       8 | Asp D GAT      53 | Gly G GGT      12
      GTC       6 |       GCC      16 |       GAC      23 |       GGC      48
      GTA      14 |       GCA      25 | Glu E GAA      64 |       GGA       7
      GTG      23 |       GCG      86 |       GAG      18 |       GGG      18
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.16376    C:0.28153    A:0.25296    G:0.30174
position  2:    T:0.28362    C:0.22091    A:0.29408    G:0.20139
position  3:    T:0.26829    C:0.25157    A:0.16516    G:0.31498

Codon frequencies under model, for use in evolver:
  0.01282791  0.01202824  0.00789666  0.01506030
  0.00999127  0.00936844  0.00615047  0.01173001
  0.01330068  0.01247155  0.00000000  0.00000000
  0.00910876  0.00854094  0.00000000  0.01069392
  0.02205308  0.02067834  0.01357553  0.02589089
  0.01717648  0.01610574  0.01057357  0.02016563
  0.02286585  0.02144045  0.01407586  0.02684510
  0.01565931  0.01468315  0.00963963  0.01838444
  0.01981502  0.01857980  0.01219782  0.02326335
  0.01543332  0.01447124  0.00950051  0.01811912
  0.02054530  0.01926456  0.01264737  0.02412072
  0.01407013  0.01319303  0.00866135  0.01651869
  0.02363610  0.02216268  0.01455001  0.02774940
  0.01840944  0.01726184  0.01133257  0.02161317
  0.02450721  0.02297949  0.01508626  0.02877210
  0.01678337  0.01573714  0.01033158  0.01970412



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               0.3147 (0.0074 0.0234)
Shig4337             1.0056 (0.0652 0.0649) 1.4363 (0.0571 0.0397)
CFT073               0.4241 (0.0074 0.0174) 0.2507 (0.0074 0.0293) 0.9143 (0.0652 0.0714)
O157                 0.1792 (0.0074 0.0412) 0.1373 (0.0074 0.0536) 0.6806 (0.0643 0.0944) 0.1561 (0.0074 0.0472)
EDL933               0.1792 (0.0074 0.0412) 0.1373 (0.0074 0.0536) 0.6806 (0.0643 0.0944) 0.1561 (0.0074 0.0472)-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):  -1267.106586     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.01327  0.02243  0.00000  0.22741  0.00000  0.01775  0.03681  0.00000  0.00000  2.18992  0.88837  0.00000  0.00000 12.24839
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.31769

((1: 0.013274, (2: 0.000004, 3: 0.227409): 0.022430): 0.000000, (4: 0.017753, (5: 0.000004, 6: 0.000004): 0.036812): 0.000000);

((K12: 0.013274, (S2457T: 0.000004, Shig4337: 0.227409): 0.022430): 0.000000, (CFT073: 0.017753, (O157: 0.000004, EDL933: 0.000004): 0.036812): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.18992


dN/dS for site classes (K=3)

p:   0.88837  0.00000  0.11163
w:   0.00000  1.00000 12.24839

dN & dS for each branch

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

   7..8       0.000    192.8    527.2   1.3673   0.0000   0.0000    0.0    0.0
   8..1       0.013    192.8    527.2   1.3673   0.0048   0.0035    0.7    2.5
   8..9       0.022    192.8    527.2   1.3673   0.0081   0.0059    1.1    4.2
   9..2       0.000    192.8    527.2   1.3673   0.0000   0.0000    0.0    0.0
   9..3       0.227    192.8    527.2   1.3673   0.0817   0.0597   11.5   43.1
   7..10      0.000    192.8    527.2   1.3673   0.0000   0.0000    0.0    0.0
  10..4       0.018    192.8    527.2   1.3673   0.0064   0.0047    0.9    3.4
  10..11      0.037    192.8    527.2   1.3673   0.0132   0.0097    1.9    7.0
  11..5       0.000    192.8    527.2   1.3673   0.0000   0.0000    0.0    0.0
  11..6       0.000    192.8    527.2   1.3673   0.0000   0.0000    0.0    0.0


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

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

     2 T      1.000**       12.248
     3 P      1.000**       12.248
     4 T      1.000**       12.248
     5 I      1.000**       12.248
     6 E      1.000**       12.248
     7 L      0.768         9.408
     8 I      1.000**       12.248
     9 C      1.000**       12.248
    10 G      1.000**       12.248
    11 H      1.000**       12.248
    12 R      1.000**       12.248
    13 S      1.000**       12.248
    15 R      0.730         8.945
    16 H      1.000**       12.248
    18 T      1.000**       12.248
    19 D      1.000**       12.248
    27 R      1.000**       12.248
   117 I      1.000**       12.248
   141 K      1.000**       12.248
   172 A      1.000**       12.248
   187 G      1.000**       12.248
   188 A      1.000**       12.248
   209 R      1.000**       12.248


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

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

     2 T      0.996**       9.540 +- 1.211
     3 P      0.985*        9.444 +- 1.507
     4 T      0.979*        9.397 +- 1.627
     5 I      0.688         6.724 +- 4.262
     6 E      0.964*        9.258 +- 1.934
     7 L      0.727         7.014 +- 4.280
     8 I      0.949         9.128 +- 2.176
     9 C      0.979*        9.394 +- 1.635
    10 G      0.994**       9.522 +- 1.274
    11 H      0.994**       9.525 +- 1.264
    12 R      0.996**       9.545 +- 1.195
    13 S      0.978*        9.381 +- 1.667
    15 R      0.685         6.620 +- 4.456
    16 H      0.994**       9.520 +- 1.278
    18 T      0.695         6.795 +- 4.238
    19 D      0.955*        9.182 +- 2.080
    27 R      0.696         6.797 +- 4.234
   117 I      0.692         6.765 +- 4.247
   141 K      0.704         6.875 +- 4.203
   172 A      0.694         6.783 +- 4.241
   187 G      0.599         5.908 +- 4.483
   188 A      0.763         7.419 +- 3.939
   209 R      0.701         6.848 +- 4.214



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:   0.809  0.161  0.026  0.004  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.000  0.004  0.022  0.069  0.158  0.290  0.457

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 0.001 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 0.011 0.020 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005 0.093 0.076 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.053 0.565 0.168 0.001

sum of density on p0-p1 =   1.000000
