
seed used = 140012769

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2770.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 259
# site patterns = 86
   10    2    6   15    4   14    6    6    7   14    4    6    4    5    5
   13    1    1    1    4    1    4    1    1    1    3    1    4    5    1
    1    1    2    5    1    1    3    6    7    2    1    1    5    2    1
    1    3    4    1    1    1    1    2    1    1    1    2    3    7    4
    1    2    4    4    3    1    1    2    1    1    1    2    1    1    1
    1    1    1    1    1    1    1    1    1    1    1

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



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

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

#1: K12            
position  1:    T:0.13514    C:0.29730    A:0.20463    G:0.36293
position  2:    T:0.28571    C:0.24710    A:0.26255    G:0.20463
position  3:    T:0.21622    C:0.16988    A:0.22394    G:0.38996

#2: S2457T         
position  1:    T:0.13514    C:0.29730    A:0.20077    G:0.36680
position  2:    T:0.28571    C:0.24710    A:0.25869    G:0.20849
position  3:    T:0.21622    C:0.17375    A:0.22008    G:0.38996

#3: Shig4337       
position  1:    T:0.13514    C:0.29730    A:0.20077    G:0.36680
position  2:    T:0.28571    C:0.24710    A:0.25869    G:0.20849
position  3:    T:0.21622    C:0.17375    A:0.22008    G:0.38996

#4: CFT073         
position  1:    T:0.14729    C:0.28682    A:0.20543    G:0.36047
position  2:    T:0.28295    C:0.24806    A:0.26357    G:0.20543
position  3:    T:0.20930    C:0.17829    A:0.20930    G:0.40310

#5: O157           
position  1:    T:0.13900    C:0.29730    A:0.20463    G:0.35907
position  2:    T:0.28185    C:0.25097    A:0.25869    G:0.20849
position  3:    T:0.22394    C:0.16602    A:0.21236    G:0.39768

#6: EDL933         
position  1:    T:0.13900    C:0.29730    A:0.20463    G:0.35907
position  2:    T:0.28185    C:0.25097    A:0.25869    G:0.20849
position  3:    T:0.22394    C:0.16602    A:0.21236    G:0.39768

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      36 | Ser S TCT       6 | Tyr Y TAT      12 | Cys C TGT      14
      TTC      12 |       TCC       0 |       TAC       2 |       TGC      23
Leu L TTA      26 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG      45 |       TCG       9 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT       7 | Pro P CCT       8 | His H CAT      14 | Arg R CGT      30
      CTC      24 |       CCC       4 |       CAC       6 |       CGC      45
      CTA      11 |       CCA      24 | Gln Q CAA      42 |       CGA      18
      CTG      96 |       CCG      36 |       CAG      82 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      41 | Thr T ACT      19 | Asn N AAT      17 | Ser S AGT       6
      ATC      12 |       ACC      23 |       AAC      13 |       AGC      24
      ATA       6 |       ACA       0 | Lys K AAA      37 | Arg R AGA      12
Met M ATG      64 |       ACG      30 |       AAG       6 |       AGG       6
------------------------------------------------------------------------------
Val V GTT      13 | Ala A GCT      50 | Asp D GAT      41 | Gly G GGT      24
      GTC       6 |       GCC      48 |       GAC      12 |       GGC      12
      GTA      18 |       GCA      29 | Glu E GAA      89 |       GGA      24
      GTG      24 |       GCG     100 |       GAG      31 |       GGG      42
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.13844    C:0.29556    A:0.20348    G:0.36252
position  2:    T:0.28397    C:0.24855    A:0.26014    G:0.20734
position  3:    T:0.21764    C:0.17128    A:0.21636    G:0.39472

Codon frequencies under model, for use in evolver:
  0.00880462  0.00692908  0.00875252  0.01596814
  0.00770654  0.00606491  0.00766094  0.01397665
  0.00806591  0.00634773  0.00000000  0.00000000
  0.00642877  0.00505933  0.00000000  0.01165928
  0.01879684  0.01479278  0.01868561  0.03409012
  0.01645256  0.01294787  0.01635521  0.02983852
  0.01721978  0.01355166  0.01711788  0.03122995
  0.01372467  0.01080107  0.01364346  0.02489120
  0.01294074  0.01018413  0.01286417  0.02346945
  0.01132682  0.00891400  0.01125979  0.02054242
  0.01185501  0.00932968  0.01178486  0.02150036
  0.00944879  0.00743603  0.00939288  0.01713642
  0.02305581  0.01814452  0.02291939  0.04181424
  0.02018037  0.01588159  0.02006096  0.03659931
  0.02112143  0.01662219  0.02099645  0.03830602
  0.01683440  0.01324838  0.01673479  0.03053103



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               0.3275 (0.0052 0.0157)
Shig4337             0.3275 (0.0052 0.0157)-1.0000 (0.0000 0.0000)
CFT073               0.2940 (0.0218 0.0741) 0.2940 (0.0200 0.0681) 0.2940 (0.0200 0.0681)
O157                 0.2506 (0.0121 0.0482) 0.2432 (0.0104 0.0426) 0.2432 (0.0104 0.0426) 0.4467 (0.0253 0.0567)
EDL933               0.2506 (0.0121 0.0482) 0.2432 (0.0104 0.0426) 0.2432 (0.0104 0.0426) 0.4467 (0.0253 0.0567)-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):  -1260.926203     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.01800  0.00714  0.00000  0.00000  0.02510  0.09258  0.03188  0.00000  0.00000  3.04342  0.98302  0.00000  0.27191 23.06000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.17472

((1: 0.017997, (2: 0.000004, 3: 0.000004): 0.007144): 0.000000, (4: 0.092585, (5: 0.000004, 6: 0.000004): 0.031877): 0.025102);

((K12: 0.017997, (S2457T: 0.000004, Shig4337: 0.000004): 0.007144): 0.000000, (CFT073: 0.092585, (O157: 0.000004, EDL933: 0.000004): 0.031877): 0.025102);

Detailed output identifying parameters

kappa (ts/tv) =  3.04342


dN/dS for site classes (K=3)

p:   0.98302  0.00000  0.01698
w:   0.27191  1.00000 23.06000

dN & dS for each branch

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

   7..8       0.000    231.3    545.7   0.6588   0.0000   0.0000    0.0    0.0
   8..1       0.018    231.3    545.7   0.6588   0.0052   0.0079    1.8    2.8
   8..9       0.007    231.3    545.7   0.6588   0.0021   0.0031    0.7    1.1
   9..2       0.000    231.3    545.7   0.6588   0.0000   0.0000    0.0    0.0
   9..3       0.000    231.3    545.7   0.6588   0.0000   0.0000    0.0    0.0
   7..10      0.025    231.3    545.7   0.6588   0.0072   0.0110    2.5    4.0
  10..4       0.093    231.3    545.7   0.6588   0.0267   0.0406    9.4   14.6
  10..11      0.032    231.3    545.7   0.6588   0.0092   0.0140    3.2    5.0
  11..5       0.000    231.3    545.7   0.6588   0.0000   0.0000    0.0    0.0
  11..6       0.000    231.3    545.7   0.6588   0.0000   0.0000    0.0    0.0


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

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

    25 A      0.991**       22.845
    33 I      0.897         20.711
   113 H      0.999**       23.045


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

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

    25 A      0.946         7.629 +- 2.608
    33 I      0.856         6.985 +- 3.184
   113 H      0.978*        7.833 +- 2.337



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:   0.412  0.340  0.177  0.056  0.012  0.002  0.000  0.000  0.000  0.000
w2:   0.007  0.017  0.033  0.054  0.082  0.112  0.141  0.166  0.186  0.201

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.014
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.006 0.057
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.028 0.147
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.007 0.087 0.224
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.005 0.022 0.162 0.229

sum of density on p0-p1 =   1.000000
