
seed used = 139995665

K12                                  ATG ATG AAG CGC AAT ATT CTG GCA GTG ATC GTC CCT GCT CTG TTA GTA GCA GGT ACT GCA AAC GCT GCA GAA ATC TAT AAC AAA GAT GGC AAC AAA GTA GAT CTG TAC GGT AAA GCT GTT GGT CTG CAT TAT TTT TCC AAG GGT AAC GGT GAA AAC AGT TAC GGT GGC AAT GGC GAC ATG ACC TAT GCC CGT CTT GGT TTT AAA GGG GAA ACT CAA ATC AAT TCC GAT CTG ACC GGT TAT GGT CAG TGG GAA TAT AAC TTC CAG GGT AAC AAC TCT GAA GGC GCT GAC GCT CAA ACT GGT AAC AAA ACG CGT CTG GCA TTC GCG GGT CTT AAA TAC GCT GAC GTT GGT TCT TTC GAT TAC GGC CGT AAC TAC GGT GTG GTT TAT GAT GCA CTG GGT TAC ACC GAT ATG CTG CCA GAA TTT GGT GGT GAT ACT GCA TAC AGC GAT GAC TTC TTC GTT GGT CGT GTT GGC GGC GTT GCT ACC TAT CGT AAC TCC AAC TTC TTT GGT CTG GTT GAT GGC CTG AAC TTC GCT GTT CAG TAC CTG GGT AAA AAC GAG CGT GAC ACT GCA CGC CGT TCT AAC GGC GAC GGT GTT GGC GGT TCT ATC AGC TAC GAA TAC GAA GGC TTT GGT ATC GTT GGT GCT TAT GGT GCA GCT GAC CGT ACC AAC CTG CAA GAA GCT CAA CCT CTT GGC AAC GGT AAA AAA GCT GAA CAG TGG GCT ACT GGT CTG AAG TAC GAC GCG AAC AAC ATC TAC CTG GCA GCG AAC TAC GGT GAA ACC CGT AAC GCT ACG CCG ATC ACT AAT AAA TTT ACA AAC ACC AGC GGC TTC GCC AAC AAA ACG CAA GAC GTT CTG TTA GTT GCG CAA TAC CAG TTC GAT TTC GGT CTG CGT CCG TCC ATC GCT TAC ACC AAA TCT AAA GCG AAA GAC GTA GAA GGT ATC GGT GAT GTT GAT CTG GTG AAC TAC TTT GAA GTG GGC GCA ACC TAC TAC TTC AAC AAA AAC ATG TCC ACC TAT GTT GAC TAC ATC ATC AAC CAG ATC GAT TCT GAC AAC AAA CTG GGC GTA GGT TCA GAC GAC ACC GTT GCT GTG GGT ATC GTT TAC CAG TTC 
S2457T                               ATG ATG AAG CGC AAT ATT CTG GCA GTG ATC GTC CCT GCT CTG TTA GTA GCA GGT ACT GCA AAC GCT GCA GAA ATC TAT AAC AAA GAT GGC AAC AAA GTA GAT CTG TAC GGT AAA ACT GTT GGT CTG CAT TAT TTT TCC AAG GGT AAC GGT GAA AAC AGT TAC GGT GGC AAT GGC GAC ATG ACC TAT GCC CGT CTT GGT TTT AAA GGG GAA ACT CAA ATC AAT TCC GAT CTG ACC GGT TAT GGT CAG TGG GAA TAT AAC TTC CAG GGT AAC AAC TCT GAA GGC GCT GAC GCT CAA ACT GGT AAC AAA ACG CGT CTG GCA TTC GCG GGT CTT AAA TAC GCT GAC GTT GGT TCT TTC GAT TAC GGC CGT AAC TAC GGT GTG GTT TAT GAT GCA CTG GGT TAC ACC GAT ATG CTG CCA GAA TTT GGT GGT GAT ACT GCA TAC AGC GAT GAC TTC TTC GTT GGT CGT GTT GGC GGC GTT GCT ACC TAT CGT AAC TCC AAC TTC TTT GGT CTG GTT GAT GGC CTG AAC TTC GCT GTT CAG TAC CTG GGT AAA AAC GAG CGT GAC ACT GCA CGC CGT TCT AAC GGC GAC GGT GTT GGC GGT TCT ATC AGC TAC GAA TAC GAA GGC TTT GGT ATC GTT GGT GCT TAT GGT GCA GCT GAC CGT ACC AAC CTG CAA GAA GCT CAA CCT CTT GGC AAC GGT AAA AAA GCT GAA CAG TGG GCT ACT GGT CTG AAG TAC GAC GCG AAC AAC ATC TAC CTG GCA GCG AAC TAC GGT GAA ACC CGT AAC GCT ACG CCG ATC ACT AAT AAA TTT ACA AAC ACC AGC GGC TTC GCC AAC AAA ACG CAA GAC GTT CTG TTA GTT GCG CAA TAC CAG TTC GAT TTC GGT CTG CGT CCG TCC ATC GCT TAC ACC AAA TCT AAA GCG AAA GAC GTA GAA GGT ATC GGT GAT GTT GAT CTG GTG AAC TAC TTT GAA GTG GGC GCA ACC TAC TAC TTC AAC AAA AAC ATG TCC ACC TAT GTT GAC TAC ATC ATC AAC CAG ATC GAT TCT GAC AAC AAA CTG GGC GTA GGT TCA GAC GAC ACC GTT GCT GTG GGT ATC GTT TAC CAG TTC 
Shig4337                             ATG ATG AAG CGC AAT ATT CTG GCA GTG ATC GTC CCT GCT CTG TTA GTA GCA GGT ACT GCA AAC GCT GCA GAA ATC TAT AAC AAA GAT GGC AAC AAA GTA GAT CTG TAC GGT AAA ACT GTT GGT CTG CAT TAT TTT TCC AAG GGT AAC GGT GAA AAC AGT TAC GGT GGC AAT GGC GAC ATG ACC TAT GCC CGT CTT GGT TTT AAA GGG GAA ACT CAA ATC AAT TCC GAT CTG ACC GGT TAT GGT CAG TGG GAA TAT AAC TTC CAG GGT AAC AAC TCT GAA GGC GCT GAC GCT CAA ACT GGT AAC AAA ACG CGT CTG GCA TTC GCG GGT CTT AAA TAC GCT GAC GTT GGT TCT TTC GAT TAC GGC CGT AAC TAC GGT GTG GTT TAT GAT GCA CTG GGT TAC ACC GAT ATG CTG CCA GAA TTT GGT GGT GAT ACT GCA TAC AGC GAT GAC TTC TTC GTT GGT CGT GTT GGC GGC GTT GCT ACC TAT CGT AAC TCC AAC TTC TTT GGT CTG GTT GAT GGC CTG AAC TTC GCT GTT CAG TAC CTG GGT AAA AAC GAG CGT GAC ACT GCA CGC CGT TCT AAC GGC GAC GGT GTT GGC GGT TCT ATC AGC TAC GAA TAC GAA GGC TTT GGT ATC GTT GGT GCT TAT GGT GCA GCT GAC CGT ACC AAC CTG CAA GAA GCT CAA CCT CTT GGC AAC GGT AAA AAA GCT GAA CAG TGG GCT ACT GGT CTG AAG TAC GAC GCG AAC AAC ATC TAC CTG GCA GCG AAC TAC GGT GAA ACC CGT AAC GCT ACG CCG ATC ACT AAT AAA TTT ACA AAC ACC AGC GGC TTC GCC AAC AAA ACG CAA GAC GTT CTG TTA GTT GCG CAA TAC CAG TTC GAT TTC GGT CTG CGT CCG TCC ATC GCT TAC ACC AAA TCT AAA GCG AAA GAC GTA GAA GGT ATC GGT GAT GTT GAT CTG GTG AAC TAC TTT GAA GTG GGC GCA ACC TAC TAC TTC AAC AAA AAC ATG TCC ACC TAT GTT GAC TAC ATC ATC AAC CAG ATC GAT TCT GAC AAC AAA CTG GGC GTA GGT TCA GAC GAC ACC GTT GCT GTG GGT ATC GTT TAC CAG TTC 
CFT073                               ATG ATG AAG CGC AAT ATT CTG GCA GTG ATC GTC CCT GCT CTG TTA GTA GCA GGT ACT GCA AAC GCT GCA GAA ATC TAT AAC AAA GAT GGC AAC AAA GTA GAT CTG TAC GGT AAA GCT GTC GGT CTG CAT TAT TTC TCC AAG GGT AAC GGT GAA AAC AGT TAC GGT GGC AAT GGC GAC ATG ACC TAT GCC CGT CTT GGT TTT AAA GGG GAA ACT CAA ATC AAT TCC GAT CTG ACC GGT TAT GGT CAG TGG GAA TAT AAC TTC CAG GGT AAC AAC TCT GAG GGC GCT GAC GCT CAA ACT GGT AAC AAA ACG CGT CTG GCA TTC GCG GGT CTT AAA TAC GCT GAC GTT GGT TCT TTC GAT TAC GGC CGT AAC TAC GGT GTG GTT TAT GAT GCA CTG GGT TAC ACC GAT ATG CTG CCA GAA TTT GGT GGT GAT ACT GCA TAC AGC GAT GAT TTC TTC GTT GGT CGT GTT GGC GGC GTT GCT ACC TAT CGT AAC TCC AAC TTC TTT GGT CTG GTT GAT GGT CTG AAC TTC GCT GTT CAG TAC CTG GGT AAA AAC GAG CGT GAC ACT GCA CGC CGC TCT AAC GGC GAC GGT GTT GGC GGT TCT ATC AGC TAC GAA TAC GAA GGC TTT GGT ATC GTT GGT GCT TAT GGT GCC GCT GAC CGT ACC AAC CTG CAG GAA GAG TCT TCC CTT GGC AAA GGC AAA AAA GCT GAA CAG TGG GCT ACT GGT CTG AAG TAT GAC GCG AAC AAC ATC TAC CTG GCA GCG AAC TAC GGT GAA ACC CGT AAC GCT ACG CCG ATC ACT AAT AAA TTT ACA AAC ACC AGC GGC TTC GCC AAC AAA ACG CAA GAC GTT CTG TTA GTT GCG CAA TAC CAG TTT GAT TTC GGT CTG CGT CCG TCC ATC GCT TAC ACC AAA TCT AAA GCG AAA GAC GTA GAA GGT ATC GGT GAT GTT GAT CTG GTG AAC TAC TTT GAA GTG GGC GCA ACC TAC TAT TTC AAC AAA AAC ATG TCC ACC TAT GTT GAC TAC ATC ATC AAC CAG ATC GAT TCT GAC AAC AAA CTG GGC GTA GGT TCT GAC GAC ACC GTT GCT GTG GGT ATC GTT TAC CAG TTC 
O157                                 ATG ATG AAG CGC AAT ATT CTG GCA GTG ATC GTC CCT GCT CTG TTA GTA GCA GGT ACT GCA AAC GCT GCA GAA ATC TAT AAC AAA GAT GGC AAC AAA GTA GAT CTG TAC GGT AAA GCT GTC GGT CTG CAT TAT TTC TCC AAG GGT AAC GGT GAA AAC AGT TAC GGT GGC AAT GGC GAC ATG ACC TAT GCC CGT CTT GGT TTT AAA GGG GAA ACT CAA ATC AAT TCC GAT CTG ACC GGT TAT GGT CAG TGG GAA TAT AAC TTC CAG GGT AAC AAC TCT GAA GGC GCT GAC GCT CAA ACT GGT AAC AAA ACG CGT CTG GCA TTC GCG GGT CTT AAA TAC GCT GAC GTT GGT TCT TTC GAT TAC GGC CGT AAC TAC GGT GTG GTT TAT GAT GCA CTG GGT TAC ACC GAT ATG CTG CCA GAA TTT GGT GGT GAT ACT GCA TAC AGC GAT GAC TTC TTC GTT GGT CGT GTT GGC GGC GTT GCT ACC TAT CGT AAC TCC AAC TTC TTT GGT CTG GTT GAT GGC CTG AAC TTC GCT GTT CAG TAC CTG GGT AAA AAC GAG CGT GAC ACT GCA CGC CGC TCT AAC GGC GAC GGT GTT GGC GGT TCT ATC AGC TAC GAA TAC GAA GGC TTT GGT ATC GTT GGT GCT TAT GGT GCA GCT GAC CGT ACC AAC CTG CAA GAA GCT CAA CTT CTT GGC AAC GGT AAA AAA GCT GAA CAG TGG GCT ACT GGT CTG AAG TAT GAT GCG AAC AAC ATC TAC CTG GCA GCG AAC TAC GGT GAA ACG CGT AAC GCT ACG CCG ATC ACT AAT AAA TTT ACA AAC ATC AGC GGC TTC GCC AAC AAA ACG CAA GAC GTT CTG TTA GTT GCG CAA TAC CAG TTC GAT TTC GGT CTG CGT CCG TCC ATC GCT TAC ACC AAA TCT AAA GCG AAA GAC GTA GAA GGT ATC GGT GAT GTT GAT CTG GTG AAC TAC TTT GAA GTG GGC GCA ACC TAC TAC TTC AAC AAA AAC ATG TCC ACC TAT GTT GAC TAC ATC ATC AAC CAG ATC GAT TCT GAC AAC AAA CTG GGC GTA GGT TCA GAC GAC ACC GTT GCT GTG GGT ATC GTT TAC CAG TTC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0929.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 362
# site patterns = 67
    5    3    2    4    1   18   10    5   13    1    1   14    2    4   32
    7   27   12    9   16   13   14   18    1    1    1    1    5    1   12
    9    2    9    3    6    1    4    7    2   11    6    1    3    5   15
    1    3    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    2    1    1    1    1    1

1       
K12                   ATG AAG CGC AAT ATT CTG GCA GTG ATC GTC CCT GCT TTA GTA GGT ACT AAC GAA TAT AAA GAT GGC TAC GCT GTT CAT TTT TCC AGT GAC ACC GCC CGT CTT TTT GGG CAA CAG TGG TTC TCT GAA ACG GCG GTT CCA AGC GAC GGC GAG CGT GCA CAA GCT CAA CCT AAC GGT TAC GAC ACC CCG ACA ACC TTC TAC TCA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ..T ..T ... ..C ..C ..G .AG TCT T.C ..A ..C ..T ... ... ... ... ... ..T ..T ..T 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... .T. ... ... ..T ..T ..G ... ... .T. ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  7  7  7  7  6 | Ser TCT  6  6  6  8  6 | Tyr TAT  9  9  9 11 10 | Cys TGT  0  0  0  0  0
    TTC 12 12 12 12 13 |     TCC  5  5  5  6  5 |     TAC 20 20 20 18 19 |     TGC  0  0  0  0  0
Leu TTA  2  2  2  2  2 |     TCA  1  1  1  0  1 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  0  0  0  0  0 |     TCG  0  0  0  0  0 |     TAG  0  0  0  0  0 | Trp TGG  2  2  2  2  2
--------------------------------------------------------------------------------------------------
Leu CTT  3  3  3  3  4 | Pro CCT  2  2  2  1  1 | His CAT  1  1  1  1  1 | Arg CGT 10 10 10  9  9
    CTC  0  0  0  0  0 |     CCC  0  0  0  0  0 |     CAC  0  0  0  0  0 |     CGC  2  2  2  3  3
    CTA  0  0  0  0  0 |     CCA  1  1  1  1  1 | Gln CAA  6  6  6  4  6 |     CGA  0  0  0  0  0
    CTG 18 18 18 18 18 |     CCG  2  2  2  2  2 |     CAG  7  7  7  8  7 |     CGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Ile ATT  1  1  1  1  1 | Thr ACT  7  8  8  7  7 | Asn AAT  4  4  4  4  4 | Ser AGT  1  1  1  1  1
    ATC 13 13 13 13 14 |     ACC 11 11 11 11  9 |     AAC 28 28 28 27 28 |     AGC  3  3  3  3  3
    ATA  0  0  0  0  0 |     ACA  1  1  1  1  1 | Lys AAA 16 16 16 17 16 | Arg AGA  0  0  0  0  0
Met ATG  5  5  5  5  5 |     ACG  3  3  3  3  4 |     AAG  3  3  3  3  3 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT 16 16 16 15 15 | Ala GCT 16 15 15 15 16 | Asp GAT 13 13 13 14 14 | Gly GGT 33 33 33 33 33
    GTC  1  1  1  2  2 |     GCC  2  2  2  3  2 |     GAC 14 14 14 13 13 |     GGC 15 15 15 15 15
    GTA  4  4  4  4  4 |     GCA 11 11 11 10 11 | Glu GAA 13 13 13 12 13 |     GGA  0  0  0  0  0
    GTG  5  5  5  5  5 |     GCG  5  5  5  5  5 |     GAG  1  1  1  3  1 |     GGG  1  1  1  1  1
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.17680    C:0.14365    A:0.26519    G:0.41436
position  2:    T:0.24033    C:0.20166    A:0.37293    G:0.18508
position  3:    T:0.35635    C:0.34807    A:0.15193    G:0.14365

#2: S2457T         
position  1:    T:0.17680    C:0.14365    A:0.26796    G:0.41160
position  2:    T:0.24033    C:0.20166    A:0.37293    G:0.18508
position  3:    T:0.35635    C:0.34807    A:0.15193    G:0.14365

#3: Shig4337       
position  1:    T:0.17680    C:0.14365    A:0.26796    G:0.41160
position  2:    T:0.24033    C:0.20166    A:0.37293    G:0.18508
position  3:    T:0.35635    C:0.34807    A:0.15193    G:0.14365

#4: CFT073         
position  1:    T:0.18232    C:0.13812    A:0.26519    G:0.41436
position  2:    T:0.24033    C:0.20166    A:0.37293    G:0.18508
position  3:    T:0.35912    C:0.34807    A:0.14088    G:0.15193

#5: O157           
position  1:    T:0.17680    C:0.14365    A:0.26519    G:0.41436
position  2:    T:0.24586    C:0.19613    A:0.37293    G:0.18508
position  3:    T:0.35359    C:0.34807    A:0.15193    G:0.14641

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      34 | Ser S TCT      32 | Tyr Y TAT      48 | Cys C TGT       0
      TTC      61 |       TCC      26 |       TAC      97 |       TGC       0
Leu L TTA      10 |       TCA       4 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       0 |       TAG       0 | Trp W TGG      10
------------------------------------------------------------------------------
Leu L CTT      16 | Pro P CCT       8 | His H CAT       5 | Arg R CGT      48
      CTC       0 |       CCC       0 |       CAC       0 |       CGC      12
      CTA       0 |       CCA       5 | Gln Q CAA      28 |       CGA       0
      CTG      90 |       CCG      10 |       CAG      36 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       5 | Thr T ACT      37 | Asn N AAT      20 | Ser S AGT       5
      ATC      66 |       ACC      53 |       AAC     139 |       AGC      15
      ATA       0 |       ACA       5 | Lys K AAA      81 | Arg R AGA       0
Met M ATG      25 |       ACG      16 |       AAG      15 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      78 | Ala A GCT      77 | Asp D GAT      67 | Gly G GGT     165
      GTC       7 |       GCC      11 |       GAC      68 |       GGC      75
      GTA      20 |       GCA      54 | Glu E GAA      64 |       GGA       0
      GTG      25 |       GCG      25 |       GAG       7 |       GGG       5
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.17790    C:0.14254    A:0.26630    G:0.41326
position  2:    T:0.24144    C:0.20055    A:0.37293    G:0.18508
position  3:    T:0.35635    C:0.34807    A:0.14972    G:0.14586

Codon frequencies under model, for use in evolver:
  0.01569104  0.01532613  0.00659267  0.00642238
  0.01303398  0.01273086  0.00547629  0.00533484
  0.02423673  0.02367309  0.00000000  0.00000000
  0.01202860  0.01174887  0.00000000  0.00492333
  0.01257233  0.01227995  0.00528233  0.00514588
  0.01044337  0.01020050  0.00438784  0.00427450
  0.01941950  0.01896788  0.00815920  0.00794844
  0.00963782  0.00941369  0.00404938  0.00394478
  0.02348783  0.02294160  0.00986853  0.00961362
  0.01951049  0.01905676  0.00819743  0.00798569
  0.03627983  0.03543612  0.01524315  0.01484942
  0.01800555  0.01758681  0.00756512  0.00736971
  0.03645000  0.03560232  0.01531465  0.01491907
  0.03027769  0.02957355  0.01272132  0.01239273
  0.05630148  0.05499215  0.02365535  0.02304433
  0.02794222  0.02729240  0.01174006  0.01143681



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              -1.0000 (0.0012 0.0000)
Shig4337            -1.0000 (0.0012 0.0000)-1.0000 (0.0000 0.0000)
CFT073               0.1212 (0.0073 0.0602) 0.1415 (0.0085 0.0602) 0.1415 (0.0085 0.0602)
O157                 0.1031 (0.0024 0.0235) 0.1547 (0.0036 0.0235) 0.1547 (0.0036 0.0235) 0.1876 (0.0097 0.0519)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 22
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1571.874691     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00843  0.00000  0.00309  0.00000  0.00000  0.00745  0.06939  0.01155  3.13142  0.92560  0.06422  0.00000 36.78372
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.09993

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.003095): 0.008429, (4: 0.069391, 5: 0.011555): 0.007445);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.003095): 0.008429, (CFT073: 0.069391, O157: 0.011555): 0.007445);

Detailed output identifying parameters

kappa (ts/tv) =  3.13142


dN/dS for site classes (K=3)

p:   0.92560  0.06422  0.01017
w:   0.00000  1.00000 36.78372

dN & dS for each branch

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

   6..7       0.008    302.1    783.9   0.4384   0.0021   0.0047    1.4    1.6
   7..1       0.000    302.1    783.9   0.4384   0.0000   0.0000    0.0    0.0
   7..8       0.003    302.1    783.9   0.4384   0.0008   0.0017    0.5    0.6
   8..2       0.000    302.1    783.9   0.4384   0.0000   0.0000    0.0    0.0
   8..3       0.000    302.1    783.9   0.4384   0.0000   0.0000    0.0    0.0
   6..9       0.007    302.1    783.9   0.4384   0.0018   0.0042    1.3    1.4
   9..4       0.069    302.1    783.9   0.4384   0.0171   0.0389   11.8   13.4
   9..5       0.012    302.1    783.9   0.4384   0.0028   0.0065    2.0    2.2


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

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

   224 A      0.863         31.894
   225 Q      0.999**       36.748
   226 P      0.970*        35.718


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

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

    39 A      0.514         4.384 +- 4.104
   224 A      0.928         7.605 +- 2.709
   225 Q      0.992**       8.036 +- 2.107
   226 P      0.962*        7.852 +- 2.394
   229 N      0.504         4.300 +- 4.096
   269 T      0.590         5.004 +- 4.096



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:   0.938  0.059  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.003  0.010  0.026  0.051  0.082  0.114  0.145  0.171  0.192  0.207

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 0.001 0.073
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.021 0.899

sum of density on p0-p1 =   1.000000
