
seed used = 140033249

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4483.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 260
# site patterns = 74
    5   11   10    4    4    6    3    4    5    1    3    4   16    4    4
    5    3    1    4    3    2    2    4    1    1    1   13   11    3    8
    2    3    2    3    6    2    4    4    2    4    1    1   10    7    6
    4    3    4    4    1    6    1    1    6    2    1    1    3    3    1
    1    3    1    1    1    1    1    1    1    1    1    1    1    1

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

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

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

#1: K12            
position  1:    T:0.15769    C:0.28077    A:0.20000    G:0.36154
position  2:    T:0.27308    C:0.25769    A:0.28077    G:0.18846
position  3:    T:0.28846    C:0.21923    A:0.16923    G:0.32308

#2: S2457T         
position  1:    T:0.15769    C:0.28077    A:0.20000    G:0.36154
position  2:    T:0.27308    C:0.25769    A:0.27692    G:0.19231
position  3:    T:0.27692    C:0.21538    A:0.16538    G:0.34231

#3: Shig4337       
position  1:    T:0.15769    C:0.28077    A:0.20000    G:0.36154
position  2:    T:0.27308    C:0.25769    A:0.27692    G:0.19231
position  3:    T:0.27692    C:0.21538    A:0.16538    G:0.34231

#4: CFT073         
position  1:    T:0.15769    C:0.28077    A:0.20385    G:0.35769
position  2:    T:0.28077    C:0.25385    A:0.27692    G:0.18846
position  3:    T:0.27692    C:0.22308    A:0.16154    G:0.33846

#5: O157           
position  1:    T:0.15385    C:0.28462    A:0.20000    G:0.36154
position  2:    T:0.27308    C:0.25769    A:0.28077    G:0.18846
position  3:    T:0.28846    C:0.21923    A:0.17308    G:0.31923

#6: EDL933         
position  1:    T:0.15385    C:0.28462    A:0.20000    G:0.36154
position  2:    T:0.27308    C:0.25769    A:0.28077    G:0.18846
position  3:    T:0.28846    C:0.21923    A:0.17308    G:0.31923

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      66 | Ser S TCT       0 | Tyr Y TAT      18 | Cys C TGT      18
      TTC       0 |       TCC      12 |       TAC       0 |       TGC      19
Leu L TTA      11 |       TCA      12 | *** * TAA       0 | *** * TGA       0
      TTG      34 |       TCG      18 |       TAG       0 | Trp W TGG      36
------------------------------------------------------------------------------
Leu L CTT       9 | Pro P CCT      16 | His H CAT      27 | Arg R CGT      35
      CTC      25 |       CCC       6 |       CAC      24 |       CGC      50
      CTA      12 |       CCA      24 | Gln Q CAA      24 |       CGA       6
      CTG      78 |       CCG      38 |       CAG      48 |       CGG      18
------------------------------------------------------------------------------
Ile I ATT      60 | Thr T ACT      15 | Asn N AAT      19 | Ser S AGT       5
      ATC      24 |       ACC      31 |       AAC      29 |       AGC      19
      ATA       0 |       ACA      20 | Lys K AAA      25 | Arg R AGA       0
Met M ATG      30 |       ACG      24 |       AAG      12 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      36 | Ala A GCT      29 | Asp D GAT      63 | Gly G GGT      25
      GTC       6 |       GCC      43 |       GAC      24 |       GGC      29
      GTA      18 |       GCA      12 | Glu E GAA      77 |       GGA      21
      GTG      19 |       GCG     101 |       GAG      45 |       GGG      15
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15641    C:0.28205    A:0.20064    G:0.36090
position  2:    T:0.27436    C:0.25705    A:0.27885    G:0.18974
position  3:    T:0.28269    C:0.21859    A:0.16795    G:0.33077

Codon frequencies under model, for use in evolver:
  0.01246429  0.00963792  0.00740509  0.01458407
  0.01167799  0.00902992  0.00693795  0.01366405
  0.01266815  0.00979555  0.00000000  0.00000000
  0.00862016  0.00666548  0.00000000  0.01008618
  0.02247659  0.01737986  0.01335344  0.02629914
  0.02105867  0.01628346  0.01251105  0.02464008
  0.02284420  0.01766411  0.01357184  0.02672927
  0.01554456  0.01201971  0.00923509  0.01818819
  0.01598903  0.01236340  0.00949915  0.01870825
  0.01498037  0.01158346  0.00889991  0.01752806
  0.01625053  0.01256560  0.00965451  0.01901423
  0.01105783  0.00855039  0.00656951  0.01293842
  0.02875982  0.02223832  0.01708633  0.03365094
  0.02694553  0.02083543  0.01600846  0.03152810
  0.02923019  0.02260203  0.01736578  0.03420131
  0.01988997  0.01537977  0.01181672  0.02327262



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               0.1415 (0.0068 0.0483)
Shig4337             0.1415 (0.0068 0.0483)-1.0000 (0.0000 0.0000)
CFT073               0.2486 (0.0120 0.0483) 0.1201 (0.0051 0.0427) 0.1201 (0.0051 0.0427)
O157                 0.3263 (0.0017 0.0052) 0.0953 (0.0051 0.0538) 0.0953 (0.0051 0.0538) 0.1913 (0.0103 0.0538)
EDL933               0.3263 (0.0017 0.0052) 0.0953 (0.0051 0.0538) 0.0953 (0.0051 0.0538) 0.1913 (0.0103 0.0538)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 27
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1205.760896     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.00398  0.05515  0.00000  0.00000  0.00000  0.07088  0.00449  0.00000  0.00000  6.58747  0.92792  0.04801  0.00000 16.57113
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.13451

((1: 0.003984, (2: 0.000004, 3: 0.000004): 0.055146): 0.000000, (4: 0.070875, (5: 0.000004, 6: 0.000004): 0.004490): 0.000000);

((K12: 0.003984, (S2457T: 0.000004, Shig4337: 0.000004): 0.055146): 0.000000, (CFT073: 0.070875, (O157: 0.000004, EDL933: 0.000004): 0.004490): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  6.58747


dN/dS for site classes (K=3)

p:   0.92792  0.04801  0.02407
w:   0.00000  1.00000 16.57113

dN & dS for each branch

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

   7..8       0.000    245.0    535.0   0.4469   0.0000   0.0000    0.0    0.0
   8..1       0.004    245.0    535.0   0.4469   0.0010   0.0021    0.5    0.5
   8..9       0.055    245.0    535.0   0.4469   0.0132   0.0296    7.3    7.1
   9..2       0.000    245.0    535.0   0.4469   0.0000   0.0000    0.0    0.0
   9..3       0.000    245.0    535.0   0.4469   0.0000   0.0000    0.0    0.0
   7..10      0.000    245.0    535.0   0.4469   0.0000   0.0000    0.0    0.0
  10..4       0.071    245.0    535.0   0.4469   0.0170   0.0381    9.3    9.1
  10..11      0.004    245.0    535.0   0.4469   0.0011   0.0024    0.6    0.6
  11..5       0.000    245.0    535.0   0.4469   0.0000   0.0000    0.0    0.0
  11..6       0.000    245.0    535.0   0.4469   0.0000   0.0000    0.0    0.0


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

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

    23 C      0.680         11.582
   108 R      0.726         12.308
   119 D      0.948         15.764
   167 H      0.947         15.753
   188 E      0.627         10.764
   189 L      0.984*        16.302


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

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

    23 C      0.553         4.785 +- 4.162
   108 R      0.589         5.077 +- 4.147
   119 D      0.923         7.670 +- 2.786
   167 H      0.924         7.680 +- 2.775
   188 E      0.532         4.604 +- 4.157
   189 L      0.894         7.542 +- 3.108



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:   0.857  0.128  0.013  0.001  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.011  0.015  0.026  0.043  0.069  0.100  0.135  0.169  0.202  0.230

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.020
 0.000 0.000 0.000 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 0.152
 0.000 0.000 0.000 0.000 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 0.071 0.740

sum of density on p0-p1 =   1.000000
