
seed used = 140012045

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2700.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 165
# site patterns = 63
    4    5    2    4   10    4    6    1    1    1    2    9    4    7    5
    6    3    7    3    1    1    3    2    1    2    3    4    6    4    4
    1    1    5    2    1    4    1    2    1    1    2    2    1    1    1
    1    1    1    4    1    1    1    1    1    1    1    1    1    1    1
    2    3    1

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

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

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

#1: K12            
position  1:    T:0.12727    C:0.17576    A:0.24242    G:0.45455
position  2:    T:0.23636    C:0.27273    A:0.24242    G:0.24848
position  3:    T:0.27879    C:0.27273    A:0.16970    G:0.27879

#2: S2457T         
position  1:    T:0.12727    C:0.17576    A:0.24242    G:0.45455
position  2:    T:0.23636    C:0.27273    A:0.24242    G:0.24848
position  3:    T:0.27879    C:0.27273    A:0.16970    G:0.27879

#3: Shig4337       
position  1:    T:0.13333    C:0.16970    A:0.24242    G:0.45455
position  2:    T:0.23636    C:0.27273    A:0.24242    G:0.24848
position  3:    T:0.27879    C:0.27273    A:0.16970    G:0.27879

#4: CFT073         
position  1:    T:0.12727    C:0.17576    A:0.24242    G:0.45455
position  2:    T:0.23636    C:0.27273    A:0.24242    G:0.24848
position  3:    T:0.28485    C:0.26061    A:0.18182    G:0.27273

#5: O157           
position  1:    T:0.12727    C:0.17576    A:0.24242    G:0.45455
position  2:    T:0.24242    C:0.27273    A:0.24242    G:0.24242
position  3:    T:0.27879    C:0.27273    A:0.17576    G:0.27273

#6: EDL933         
position  1:    T:0.12727    C:0.17576    A:0.24242    G:0.45455
position  2:    T:0.24242    C:0.27273    A:0.24242    G:0.24242
position  3:    T:0.27879    C:0.27273    A:0.17576    G:0.27273

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      30 | Ser S TCT      12 | Tyr Y TAT      11 | Cys C TGT       6
      TTC       6 |       TCC       6 |       TAC       7 |       TGC       6
Leu L TTA       6 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG      12 |       TCG       0 |       TAG       0 | Trp W TGG      25
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       7 | His H CAT       6 | Arg R CGT      31
      CTC       0 |       CCC       5 |       CAC       0 |       CGC      17
      CTA       6 |       CCA       0 | Gln Q CAA      21 |       CGA       0
      CTG      26 |       CCG       6 |       CAG      39 |       CGG       9
------------------------------------------------------------------------------
Ile I ATT      24 | Thr T ACT      30 | Asn N AAT       0 | Ser S AGT      33
      ATC      12 |       ACC      42 |       AAC      12 |       AGC      15
      ATA       6 |       ACA       6 | Lys K AAA      24 | Arg R AGA       0
Met M ATG      24 |       ACG       6 |       AAG       6 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       6 | Ala A GCT      27 | Asp D GAT      24 | Gly G GGT      30
      GTC      24 |       GCC      50 |       GAC      12 |       GGC      54
      GTA      18 |       GCA      19 | Glu E GAA      60 |       GGA       6
      GTG      36 |       GCG      54 |       GAG      18 |       GGG      12
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12828    C:0.17475    A:0.24242    G:0.45455
position  2:    T:0.23838    C:0.27273    A:0.24242    G:0.24646
position  3:    T:0.27980    C:0.27071    A:0.17374    G:0.27576

Codon frequencies under model, for use in evolver:
  0.00872629  0.00844277  0.00541849  0.00860028
  0.00998347  0.00965910  0.00619912  0.00983931
  0.00887420  0.00858587  0.00000000  0.00000000
  0.00902210  0.00872896  0.00000000  0.00889182
  0.01188700  0.01150078  0.00738110  0.01171535
  0.01359953  0.01315767  0.00844448  0.01340315
  0.01208847  0.01169571  0.00750620  0.01191391
  0.01228995  0.01189064  0.00763130  0.01211248
  0.01649063  0.01595484  0.01023967  0.01625250
  0.01886640  0.01825342  0.01171488  0.01859397
  0.01677014  0.01622526  0.01041323  0.01652797
  0.01704964  0.01649568  0.01058678  0.01680344
  0.03091994  0.02991532  0.01919939  0.03047344
  0.03537451  0.03422516  0.02196540  0.03486368
  0.03144401  0.03042236  0.01952480  0.03098994
  0.03196807  0.03092940  0.01985021  0.03150644



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               0.0000 (0.0000 0.0165)
Shig4337             0.1622 (0.0027 0.0166)-1.0000 (0.0027 0.0000)
CFT073               0.0000 (0.0000 0.1142) 0.0000 (0.0000 0.1142) 0.0234 (0.0027 0.1148)
O157                 0.0454 (0.0027 0.0593) 0.0642 (0.0027 0.0419) 0.0868 (0.0040 0.0464) 0.0395 (0.0027 0.0682)
EDL933               0.0454 (0.0027 0.0593) 0.0642 (0.0027 0.0419) 0.0868 (0.0040 0.0464) 0.0395 (0.0027 0.0682)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 17
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -745.360299     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.06403  0.02304  0.00000  0.00000  0.00948  0.02224  0.13615  0.00000  0.00000  0.00000 17.98304  0.99392  0.00000  0.00000 137.67400
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.25495

((1: 0.023038, (2: 0.000004, 3: 0.009479): 0.000000): 0.064030, (4: 0.136147, (5: 0.000004, 6: 0.000004): 0.000000): 0.022243);

((K12: 0.023038, (S2457T: 0.000004, Shig4337: 0.009479): 0.000000): 0.064030, (CFT073: 0.136147, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.022243);

Detailed output identifying parameters

kappa (ts/tv) = 17.98304


dN/dS for site classes (K=3)

p:   0.99392  0.00000  0.00608
w:   0.00000  1.00000137.67400

dN & dS for each branch

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

   7..8       0.064    165.5    329.5   0.8374   0.0200   0.0239    4.0    6.6
   8..1       0.023    165.5    329.5   0.8374   0.0072   0.0086    1.4    2.4
   8..9       0.000    165.5    329.5   0.8374   0.0000   0.0000    0.0    0.0
   9..2       0.000    165.5    329.5   0.8374   0.0000   0.0000    0.0    0.0
   9..3       0.009    165.5    329.5   0.8374   0.0030   0.0035    0.6    1.0
   7..10      0.022    165.5    329.5   0.8374   0.0070   0.0083    1.4    2.3
  10..4       0.136    165.5    329.5   0.8374   0.0426   0.0509    8.4   14.0
  10..11      0.000    165.5    329.5   0.8374   0.0000   0.0000    0.0    0.0
  11..5       0.000    165.5    329.5   0.8374   0.0000   0.0000    0.0    0.0
  11..6       0.000    165.5    329.5   0.8374   0.0000   0.0000    0.0    0.0


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

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

   134 R      1.000**       137.674


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

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

   134 R      0.984*        7.321 +- 2.598



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:   0.944  0.053  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.027  0.042  0.059  0.076  0.092  0.107  0.123  0.140  0.158  0.176

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 0.005
 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 0.065
 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 0.027 0.898

sum of density on p0-p1 =   1.000000
