
seed used = 140008629

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2340.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 161
# site patterns = 76
    6    3    6    2    3    2    2    3    2    2    6    1    5    1    2
    1    3   11    2    1    1    4    4    8    1    2    2    3    2    3
    2    4    5    2    1    3    1    1    1    2    1    4    3    1    1
    1    1    2    2    1    2    2    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1

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

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

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

#1: K12            
position  1:    T:0.15528    C:0.22981    A:0.24224    G:0.37267
position  2:    T:0.31677    C:0.25466    A:0.24224    G:0.18634
position  3:    T:0.26087    C:0.26708    A:0.18012    G:0.29193

#2: S2457T         
position  1:    T:0.16149    C:0.22981    A:0.24224    G:0.36646
position  2:    T:0.31677    C:0.25466    A:0.24224    G:0.18634
position  3:    T:0.26708    C:0.25466    A:0.18012    G:0.29814

#3: Shig4337       
position  1:    T:0.16149    C:0.22981    A:0.24224    G:0.36646
position  2:    T:0.31677    C:0.25466    A:0.24224    G:0.18634
position  3:    T:0.26708    C:0.25466    A:0.18012    G:0.29814

#4: CFT073         
position  1:    T:0.16149    C:0.22981    A:0.22981    G:0.37888
position  2:    T:0.31677    C:0.24845    A:0.24845    G:0.18634
position  3:    T:0.26708    C:0.24224    A:0.21118    G:0.27950

#5: O157           
position  1:    T:0.16770    C:0.21739    A:0.23602    G:0.37888
position  2:    T:0.31677    C:0.24845    A:0.24845    G:0.18634
position  3:    T:0.26087    C:0.26708    A:0.16149    G:0.31056

#6: EDL933         
position  1:    T:0.16770    C:0.21739    A:0.23602    G:0.37888
position  2:    T:0.31677    C:0.24845    A:0.24845    G:0.18634
position  3:    T:0.26087    C:0.26708    A:0.16149    G:0.31056

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      12 | Ser S TCT      10 | Tyr Y TAT      12 | Cys C TGT      24
      TTC      12 |       TCC      11 |       TAC       0 |       TGC       6
Leu L TTA      24 |       TCA       1 | *** * TAA       0 | *** * TGA       0
      TTG      17 |       TCG      16 |       TAG       0 | Trp W TGG      12
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT      19 | His H CAT       0 | Arg R CGT      12
      CTC       6 |       CCC       6 |       CAC      12 |       CGC      12
      CTA       0 |       CCA       2 | Gln Q CAA      20 |       CGA       6
      CTG      73 |       CCG      33 |       CAG      11 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       7 | Thr T ACT       8 | Asn N AAT      15 | Ser S AGT      17
      ATC      23 |       ACC      22 |       AAC      24 |       AGC      24
      ATA       0 |       ACA       9 | Lys K AAA      21 | Arg R AGA       0
Met M ATG      36 |       ACG      18 |       AAG       6 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      46 | Ala A GCT      11 | Asp D GAT      30 | Gly G GGT      26
      GTC      12 |       GCC      45 |       GAC      12 |       GGC      23
      GTA      15 |       GCA      17 | Glu E GAA      52 |       GGA       6
      GTG      17 |       GCG      15 |       GAG      22 |       GGG      12
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16253    C:0.22567    A:0.23810    G:0.37371
position  2:    T:0.31677    C:0.25155    A:0.24534    G:0.18634
position  3:    T:0.26398    C:0.25880    A:0.17909    G:0.29814

Codon frequencies under model, for use in evolver:
  0.01393098  0.01365782  0.00945121  0.01573381
  0.01106283  0.01084592  0.00750537  0.01249449
  0.01078968  0.01057811  0.00000000  0.00000000
  0.00819469  0.00803401  0.00000000  0.00925518
  0.01934365  0.01896436  0.01312334  0.02184694
  0.01536113  0.01505993  0.01042147  0.01734904
  0.01498184  0.01468808  0.01016415  0.01692067
  0.01137862  0.01115551  0.00771961  0.01285114
  0.02040844  0.02000827  0.01384572  0.02304953
  0.01620670  0.01588892  0.01099513  0.01830404
  0.01580653  0.01549660  0.01072365  0.01785208
  0.01200496  0.01176957  0.00814454  0.01355855
  0.03203237  0.03140428  0.02173177  0.03617774
  0.02543747  0.02493870  0.01725758  0.02872938
  0.02480939  0.02432293  0.01683147  0.02802001
  0.01884257  0.01847311  0.01278339  0.02128102



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               0.1663 (0.0028 0.0167)
Shig4337             0.1663 (0.0028 0.0167)-1.0000 (0.0000 0.0000)
CFT073               0.0963 (0.0111 0.1157) 0.1206 (0.0140 0.1157) 0.1206 (0.0140 0.1157)
O157                 0.0660 (0.0083 0.1262) 0.0881 (0.0111 0.1261) 0.0881 (0.0111 0.1261) 0.0312 (0.0055 0.1772)
EDL933               0.0660 (0.0083 0.1262) 0.0881 (0.0111 0.1261) 0.0881 (0.0111 0.1261) 0.0312 (0.0055 0.1772)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 28
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -806.877155     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00506  0.00743  0.01468  0.00000  0.00000  0.03124  0.11410  0.10971  0.00000  0.00000  2.86646  0.99358  0.00000  0.04985 41.79144
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.28224

((1: 0.007434, (2: 0.000004, 3: 0.000004): 0.014679): 0.005058, (4: 0.114103, (5: 0.000004, 6: 0.000004): 0.109712): 0.031237);

((K12: 0.007434, (S2457T: 0.000004, Shig4337: 0.000004): 0.014679): 0.005058, (CFT073: 0.114103, (O157: 0.000004, EDL933: 0.000004): 0.109712): 0.031237);

Detailed output identifying parameters

kappa (ts/tv) =  2.86646


dN/dS for site classes (K=3)

p:   0.99358  0.00000  0.00642
w:   0.04985  1.00000 41.79144

dN & dS for each branch

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

   7..8       0.005    144.2    338.8   0.3180   0.0010   0.0032    0.5    0.3
   8..1       0.007    144.2    338.8   0.3180   0.0015   0.0048    0.7    0.5
   8..9       0.015    144.2    338.8   0.3180   0.0030   0.0094    1.4    1.0
   9..2       0.000    144.2    338.8   0.3180   0.0000   0.0000    0.0    0.0
   9..3       0.000    144.2    338.8   0.3180   0.0000   0.0000    0.0    0.0
   7..10      0.031    144.2    338.8   0.3180   0.0063   0.0200    2.9    2.2
  10..4       0.114    144.2    338.8   0.3180   0.0232   0.0729   10.5    7.9
  10..11      0.110    144.2    338.8   0.3180   0.0223   0.0701   10.1    7.6
  11..5       0.000    144.2    338.8   0.3180   0.0000   0.0000    0.0    0.0
  11..6       0.000    144.2    338.8   0.3180   0.0000   0.0000    0.0    0.0


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

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

   145 T      1.000**       41.791


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

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

   145 T      0.969*        6.563 +- 2.845



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:   0.976  0.023  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.056  0.074  0.086  0.094  0.099  0.105  0.111  0.117  0.125  0.133

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 0.001
 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 0.038
 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 0.938

sum of density on p0-p1 =   1.000000
