
seed used = 139995805

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1025.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 475
# site patterns = 108
   13   11   14    7   13   15    1   21   14    6    5   15   11    5   21
    6    5    1   17    1   19    6    1    8    4    1    9    2    4    9
    6    1    7    8    9    6    4    6    3    5    6    3    1    1    6
    1    1    6    1    5    1    4   12    5    2   23    1    1    3    2
    4    4    1    1    2    1    1    1    4    1    1    1    1    3    5
    1    1    1    1    1    2    1    5    1    1    1    1    1    1    2
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1

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



Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT 24 22 24 24 | Ser TCT  2  2  2  2 | Tyr TAT 14 13 14 14 | Cys TGT  4  4  4  4
    TTC  4  5  4  4 |     TCC  2  3  2  2 |     TAC  6  6  6  6 |     TGC  4  4  4  4
Leu TTA 16 15 16 16 |     TCA  6  5  6  6 | *** TAA  0  0  0  0 | *** TGA  0  0  0  0
    TTG 15 15 15 15 |     TCG  1  1  1  1 |     TAG  0  0  0  0 | Trp TGG  6  6  6  6
--------------------------------------------------------------------------------------
Leu CTT  6  8  5  5 | Pro CCT  2  3  2  2 | His CAT  4  4  4  4 | Arg CGT  6  6  6  6
    CTC  0  0  0  0 |     CCC  1  0  1  1 |     CAC  3  3  3  3 |     CGC  5  6  5  5
    CTA  2  3  3  3 |     CCA  6  4  5  5 | Gln CAA  6  6  5  5 |     CGA  4  2  4  4
    CTG  8  6  8  8 |     CCG  2  2  2  2 |     CAG  8  8  8  8 |     CGG  1  2  1  1
--------------------------------------------------------------------------------------
Ile ATT 21 24 21 21 | Thr ACT  8  6  8  8 | Asn AAT 22 19 22 22 | Ser AGT 14 15 15 15
    ATC  9  9  9  9 |     ACC  9 10  9  9 |     AAC  7  7  7  7 |     AGC  6  6  5  5
    ATA 13 13 13 13 |     ACA  5  5  5  5 | Lys AAA 14 18 16 16 | Arg AGA  2  1  2  2
Met ATG 13 13 13 13 |     ACG  4  5  4  4 |     AAG  3  5  3  3 |     AGG  4  3  4  4
--------------------------------------------------------------------------------------
Val GTT 19 21 19 19 | Ala GCT  9  7  9  9 | Asp GAT 10 10 10 10 | Gly GGT  2  2  2  2
    GTC  7  7  7  7 |     GCC  4  5  4  4 |     GAC  7  8  7  7 |     GGC  7  5  7  7
    GTA  7  8  6  6 |     GCA  6  8  6  6 | Glu GAA 12 12 11 11 |     GGA  1  2  2  2
    GTG 16 11 16 16 |     GCG  6  5  7  7 |     GAG 11 11 10 10 |     GGG  6  7  7  7
--------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.23009    C:0.14159    A:0.34071    G:0.28761
position  2:    T:0.39823    C:0.16150    A:0.28097    G:0.15929
position  3:    T:0.36947    C:0.17920    A:0.22124    G:0.23009

#2: CFT073         
position  1:    T:0.22345    C:0.13938    A:0.35177    G:0.28540
position  2:    T:0.39823    C:0.15708    A:0.28761    G:0.15708
position  3:    T:0.36726    C:0.18584    A:0.22566    G:0.22124

#3: O157           
position  1:    T:0.23009    C:0.13717    A:0.34513    G:0.28761
position  2:    T:0.39602    C:0.16150    A:0.27876    G:0.16372
position  3:    T:0.36947    C:0.17699    A:0.22124    G:0.23230

#4: EDL933         
position  1:    T:0.23009    C:0.13717    A:0.34513    G:0.28761
position  2:    T:0.39602    C:0.16150    A:0.27876    G:0.16372
position  3:    T:0.36947    C:0.17699    A:0.22124    G:0.23230

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      94 | Ser S TCT       8 | Tyr Y TAT      55 | Cys C TGT      16
      TTC      17 |       TCC       9 |       TAC      24 |       TGC      16
Leu L TTA      63 |       TCA      23 | *** * TAA       0 | *** * TGA       0
      TTG      60 |       TCG       4 |       TAG       0 | Trp W TGG      24
------------------------------------------------------------------------------
Leu L CTT      24 | Pro P CCT       9 | His H CAT      16 | Arg R CGT      24
      CTC       0 |       CCC       3 |       CAC      12 |       CGC      21
      CTA      11 |       CCA      20 | Gln Q CAA      22 |       CGA      14
      CTG      30 |       CCG       8 |       CAG      32 |       CGG       5
------------------------------------------------------------------------------
Ile I ATT      87 | Thr T ACT      30 | Asn N AAT      85 | Ser S AGT      59
      ATC      36 |       ACC      37 |       AAC      28 |       AGC      22
      ATA      52 |       ACA      20 | Lys K AAA      64 | Arg R AGA       7
Met M ATG      52 |       ACG      17 |       AAG      14 |       AGG      15
------------------------------------------------------------------------------
Val V GTT      78 | Ala A GCT      34 | Asp D GAT      40 | Gly G GGT       8
      GTC      28 |       GCC      17 |       GAC      29 |       GGC      26
      GTA      27 |       GCA      26 | Glu E GAA      46 |       GGA       7
      GTG      59 |       GCG      25 |       GAG      42 |       GGG      27
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.22843    C:0.13883    A:0.34569    G:0.28706
position  2:    T:0.39712    C:0.16040    A:0.28153    G:0.16095
position  3:    T:0.36892    C:0.17976    A:0.22235    G:0.22898

Codon frequencies under model, for use in evolver:
  0.03475910  0.01693659  0.02094926  0.02157462
  0.01403919  0.00684069  0.00846140  0.00871398
  0.02464120  0.01200658  0.00000000  0.00000000
  0.01408760  0.00686427  0.00000000  0.00874403
  0.02112478  0.01029318  0.01273188  0.01311193
  0.00853229  0.00415741  0.00514240  0.00529591
  0.01497565  0.00729698  0.00902580  0.00929523
  0.00856172  0.00417175  0.00516013  0.00531417
  0.05260155  0.02563044  0.03170288  0.03264924
  0.02124575  0.01035213  0.01280479  0.01318702
  0.03728996  0.01816977  0.02247461  0.02314549
  0.02131901  0.01038782  0.01284894  0.01323249
  0.04368033  0.02128352  0.02632607  0.02711193
  0.01764247  0.00859641  0.01063309  0.01095050
  0.03096558  0.01508818  0.01866291  0.01922001
  0.01770331  0.00862605  0.01066976  0.01098826



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                 
CFT073               0.4217 (0.0339 0.0805)
O157                 0.5747 (0.0057 0.0100) 0.3644 (0.0320 0.0878)
EDL933               0.5747 (0.0057 0.0100) 0.3644 (0.0320 0.0878)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):  -2124.704601     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
  0.00296  0.01075  0.21747  0.01151  0.00000  0.00000  2.84032  0.97950  0.00000  0.33289 42.65607
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.24270

(1: 0.002960, (2: 0.217475, (3: 0.000004, 4: 0.000004): 0.011506): 0.010749);

(K12: 0.002960, (CFT073: 0.217475, (O157: 0.000004, EDL933: 0.000004): 0.011506): 0.010749);

Detailed output identifying parameters

kappa (ts/tv) =  2.84032


dN/dS for site classes (K=3)

p:   0.97950  0.00000  0.02050
w:   0.33289  1.00000 42.65607

dN & dS for each branch

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

   5..1       0.003    366.9   1058.1   1.2007   0.0010   0.0009    0.3    1.1
   5..6       0.011    366.9   1058.1   1.2007   0.0037   0.0031    1.1    4.0
   6..2       0.217    366.9   1058.1   1.2007   0.0758   0.0631   23.1   80.2
   6..7       0.012    366.9   1058.1   1.2007   0.0040   0.0033    1.2    4.2
   7..3       0.000    366.9   1058.1   1.2007   0.0000   0.0000    0.0    0.0
   7..4       0.000    366.9   1058.1   1.2007   0.0000   0.0000    0.0    0.0


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

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

    33 G      0.972*        41.486
   435 E      0.940         40.126
   472 C      0.980*        41.789
   473 E      0.832         35.563
   474 S      0.999**       42.623
   475 P      0.997**       42.533


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

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

    33 G      0.930         8.509 +- 2.602
   306 P      0.503         4.839 +- 4.351
   435 E      0.903         8.286 +- 2.866
   446 R      0.522         5.006 +- 4.356
   472 C      0.918         8.411 +- 2.726
   473 E      0.876         8.060 +- 3.090
   474 S      0.971*        8.851 +- 2.086
   475 P      0.957*        8.735 +- 2.283



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:   0.397  0.340  0.190  0.061  0.010  0.001  0.000  0.000  0.000  0.000
w2:   0.001  0.003  0.008  0.016  0.030  0.056  0.100  0.164  0.252  0.370

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 0.015
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008 0.068
 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 0.134
 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 0.005 0.171 0.139
 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 0.003 0.022 0.249 0.125

sum of density on p0-p1 =   1.000000
